Starting phenix.real_space_refine on Wed Feb 14 20:25:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rai_4776/02_2024/6rai_4776_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rai_4776/02_2024/6rai_4776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rai_4776/02_2024/6rai_4776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rai_4776/02_2024/6rai_4776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rai_4776/02_2024/6rai_4776_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rai_4776/02_2024/6rai_4776_updated.pdb" } resolution = 2.9 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6566 2.51 5 N 1797 2.21 5 O 1795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10191 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4701 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 24, 'TRANS': 562} Chain: "B" Number of atoms: 4523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4523 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} 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: 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} 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} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.80, per 1000 atoms: 0.57 Number of scatterers: 10191 At special positions: 0 Unit cell: (103.392, 81.852, 156.165, 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 6 15.00 Mg 2 11.99 O 1795 8.00 N 1797 7.00 C 6566 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: 3.86 Conformation dependent library (CDL) restraints added in 1.9 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: 2342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 9 sheets defined 58.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 3.874A pdb=" N ARG A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Proline residue: A 24 - end of helix removed outlier: 5.691A pdb=" N LEU A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 65 through 119 removed outlier: 3.560A pdb=" N ARG A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.683A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 172 removed outlier: 3.936A pdb=" N PHE A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 221 removed outlier: 3.903A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.894A pdb=" N SER A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 232 through 284 removed outlier: 3.526A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.585A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 283 " --> pdb=" O GLY A 279 " (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: 3.670A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.545A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (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 481 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 499 through 511 Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.684A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.658A pdb=" N ALA A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 38 Proline residue: B 15 - end of helix removed outlier: 4.140A pdb=" N ARG B 19 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR B 20 " --> pdb=" O TYR B 16 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 58 through 104 removed outlier: 3.779A pdb=" N ALA B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.528A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 159 through 206 removed outlier: 4.866A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 4.254A pdb=" N ALA B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.709A pdb=" N LEU B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 269 removed outlier: 3.866A pdb=" N GLY B 250 " --> pdb=" O HIS B 246 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 316 removed outlier: 4.434A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.646A pdb=" N GLY B 294 " --> pdb=" O TRP B 290 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.773A 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 382 Processing helix chain 'B' and resid 407 through 413 removed outlier: 3.640A pdb=" N LYS B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 434 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 454 through 457 No H-bonds generated for 'chain 'B' and resid 454 through 457' 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 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 507 through 519 removed outlier: 3.888A pdb=" N THR B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 removed outlier: 4.176A pdb=" N HIS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 Processing helix chain 'B' and resid 564 through 574 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 Processing sheet with id= B, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.655A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 564 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER A 549 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU A 391 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 551 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLY A 393 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 removed outlier: 7.868A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 394 through 397 removed outlier: 4.846A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 549 through 554 removed outlier: 6.852A pdb=" N VAL B 544 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 553 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 542 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 541 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR B 526 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE B 369 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 528 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N GLY B 371 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 346 through 348 removed outlier: 6.912A pdb=" N ARG B 348 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TRP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.660A 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) 535 hydrogen bonds defined for protein. 1578 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: 2.95 Time building geometry restraints manager: 4.22 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: 1610 1.31 - 1.43: 2806 1.43 - 1.56: 5915 1.56 - 1.69: 22 1.69 - 1.81: 45 Bond restraints: 10398 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" N PRO B 320 " pdb=" CD PRO B 320 " ideal model delta sigma weight residual 1.473 1.562 -0.089 1.40e-02 5.10e+03 4.08e+01 bond pdb=" N PRO A 443 " pdb=" CD PRO A 443 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.95e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.87e+01 ... (remaining 10393 not shown) Histogram of bond angle deviations from ideal: 99.94 - 107.07: 421 107.07 - 114.19: 5659 114.19 - 121.32: 5429 121.32 - 128.44: 2510 128.44 - 135.57: 89 Bond angle restraints: 14108 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 122.72 17.15 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 128.10 8.73 1.00e+00 1.00e+00 7.62e+01 angle pdb=" N LEU B 45 " pdb=" CA LEU B 45 " pdb=" C LEU B 45 " ideal model delta sigma weight residual 111.28 120.38 -9.10 1.09e+00 8.42e-01 6.97e+01 ... (remaining 14103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 5925 17.37 - 34.75: 220 34.75 - 52.12: 44 52.12 - 69.49: 9 69.49 - 86.86: 9 Dihedral angle restraints: 6207 sinusoidal: 2547 harmonic: 3660 Sorted by residual: dihedral pdb=" C HIS A 579 " pdb=" N HIS A 579 " pdb=" CA HIS A 579 " pdb=" CB HIS A 579 " ideal model delta harmonic sigma weight residual -122.60 -138.97 16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" N HIS A 579 " pdb=" C HIS A 579 " pdb=" CA HIS A 579 " pdb=" CB HIS A 579 " ideal model delta harmonic sigma weight residual 122.80 135.97 -13.17 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" C ARG A 560 " pdb=" N ARG A 560 " pdb=" CA ARG A 560 " pdb=" CB ARG A 560 " ideal model delta harmonic sigma weight residual -122.60 -134.25 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1374 0.108 - 0.216: 191 0.216 - 0.325: 29 0.325 - 0.433: 9 0.433 - 0.541: 3 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA HIS A 579 " pdb=" N HIS A 579 " pdb=" C HIS A 579 " pdb=" CB HIS A 579 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA LEU C 104 " pdb=" N LEU C 104 " pdb=" C LEU C 104 " pdb=" CB LEU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 1603 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 231 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LYS A 231 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS A 231 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 232 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 154 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" C GLY A 154 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY A 154 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 155 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 287 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ALA A 287 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA A 287 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 288 " -0.017 2.00e-02 2.50e+03 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 53 2.54 - 3.13: 7277 3.13 - 3.72: 15559 3.72 - 4.31: 22879 4.31 - 4.90: 38180 Nonbonded interactions: 83948 Sorted by model distance: nonbonded pdb="MG MG A 702 " pdb=" O HOH A 802 " model vdw 1.948 2.170 nonbonded pdb="MG MG A 702 " pdb=" O HOH A 801 " model vdw 2.077 2.170 nonbonded pdb=" OG SER B 378 " pdb="MG MG B 602 " model vdw 2.094 2.170 nonbonded pdb="MG MG B 602 " pdb=" O HOH B 701 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.114 2.170 ... (remaining 83943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 3.910 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 30.350 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.009 0.089 10398 Z= 0.575 Angle : 1.397 18.755 14108 Z= 0.971 Chirality : 0.083 0.541 1606 Planarity : 0.008 0.056 1783 Dihedral : 10.559 86.864 3859 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.51 % 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: -3.24 (0.19), residues: 1275 helix: -2.17 (0.15), residues: 756 sheet: 0.02 (0.47), residues: 120 loop : -2.43 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 22 HIS 0.006 0.001 HIS A 121 PHE 0.039 0.003 PHE A 304 TYR 0.028 0.003 TYR B 284 ARG 0.006 0.001 ARG B 240 *********************** 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 271 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.136 Fit side-chains REVERT: A 37 LEU cc_start: 0.8211 (tp) cc_final: 0.7975 (tp) REVERT: A 58 LEU cc_start: 0.8143 (mt) cc_final: 0.7859 (mp) REVERT: A 96 TYR cc_start: 0.8440 (t80) cc_final: 0.7886 (t80) REVERT: A 145 ASN cc_start: 0.8889 (t0) cc_final: 0.8658 (t0) REVERT: A 168 PHE cc_start: 0.8304 (t80) cc_final: 0.8080 (t80) REVERT: A 206 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7685 (mpt180) REVERT: A 238 LYS cc_start: 0.8330 (mttt) cc_final: 0.7798 (mttp) REVERT: A 357 ASP cc_start: 0.7979 (t70) cc_final: 0.7552 (t0) REVERT: A 388 LYS cc_start: 0.7429 (mttt) cc_final: 0.6849 (mttm) REVERT: A 425 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7324 (mtm-85) REVERT: A 431 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7484 (mp0) REVERT: A 536 LEU cc_start: 0.8038 (pp) cc_final: 0.7705 (mp) REVERT: A 555 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7619 (mtt180) REVERT: B 131 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6999 (mm-30) REVERT: B 299 MET cc_start: 0.7514 (mmt) cc_final: 0.6947 (mmt) REVERT: B 510 GLU cc_start: 0.6683 (tt0) cc_final: 0.6441 (pp20) REVERT: B 532 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6947 (mmm160) REVERT: C 39 GLN cc_start: 0.7757 (tt0) cc_final: 0.7403 (tp40) REVERT: C 65 LYS cc_start: 0.7938 (ptmm) cc_final: 0.7712 (pttt) REVERT: C 98 THR cc_start: 0.7947 (m) cc_final: 0.7552 (p) outliers start: 0 outliers final: 1 residues processed: 271 average time/residue: 1.6790 time to fit residues: 479.5105 Evaluate side-chains 167 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 99 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 103 GLN A 146 GLN A 302 GLN A 305 GLN A 308 GLN A 318 GLN A 429 GLN A 503 GLN A 537 GLN B 111 HIS B 113 HIS B 191 GLN B 431 ASN B 538 HIS C 77 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10398 Z= 0.161 Angle : 0.560 7.588 14108 Z= 0.289 Chirality : 0.040 0.148 1606 Planarity : 0.005 0.042 1783 Dihedral : 7.499 81.921 1506 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.81 % Allowed : 11.83 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1275 helix: -0.38 (0.18), residues: 783 sheet: 0.25 (0.47), residues: 125 loop : -1.88 (0.27), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 36 HIS 0.004 0.001 HIS A 476 PHE 0.015 0.001 PHE A 304 TYR 0.022 0.001 TYR A 589 ARG 0.007 0.000 ARG A 195 *********************** 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 211 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7246 (mtt90) cc_final: 0.6792 (ttp-110) REVERT: A 33 LEU cc_start: 0.8512 (mp) cc_final: 0.8205 (mm) REVERT: A 41 LEU cc_start: 0.8221 (mt) cc_final: 0.7958 (mt) REVERT: A 96 TYR cc_start: 0.8395 (t80) cc_final: 0.7981 (t80) REVERT: A 118 MET cc_start: 0.8653 (mmp) cc_final: 0.8128 (mmp) REVERT: A 145 ASN cc_start: 0.8894 (t0) cc_final: 0.8688 (t0) REVERT: A 146 GLN cc_start: 0.7727 (mp-120) cc_final: 0.7448 (mp10) REVERT: A 206 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7558 (mpt180) REVERT: A 308 GLN cc_start: 0.7914 (mt0) cc_final: 0.7686 (mt0) REVERT: A 357 ASP cc_start: 0.7924 (t70) cc_final: 0.7692 (t70) REVERT: A 425 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7320 (mtm-85) REVERT: A 426 ARG cc_start: 0.7142 (mmp-170) cc_final: 0.6871 (mmp-170) REVERT: A 467 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7246 (mp0) REVERT: B 494 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8284 (mttm) REVERT: B 549 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7491 (mtt180) REVERT: C 39 GLN cc_start: 0.7792 (tt0) cc_final: 0.7404 (tp40) REVERT: C 82 GLN cc_start: 0.6618 (tp40) cc_final: 0.6288 (tp40) REVERT: C 83 MET cc_start: 0.7207 (mtm) cc_final: 0.6694 (mpp) outliers start: 19 outliers final: 6 residues processed: 203 average time/residue: 1.5258 time to fit residues: 328.3695 Evaluate side-chains 166 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10398 Z= 0.183 Angle : 0.533 7.796 14108 Z= 0.271 Chirality : 0.039 0.164 1606 Planarity : 0.004 0.043 1783 Dihedral : 6.527 86.157 1504 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.39 % Allowed : 14.89 % Favored : 82.73 % 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: -0.26 (0.22), residues: 1275 helix: 0.41 (0.18), residues: 784 sheet: 0.36 (0.45), residues: 125 loop : -1.48 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 36 HIS 0.002 0.001 HIS B 246 PHE 0.014 0.001 PHE A 304 TYR 0.015 0.001 TYR A 588 ARG 0.008 0.000 ARG B 218 *********************** 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 187 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.212 Fit side-chains REVERT: A 20 ARG cc_start: 0.7335 (mtt90) cc_final: 0.6932 (ttp-110) REVERT: A 33 LEU cc_start: 0.8441 (mp) cc_final: 0.8225 (mm) REVERT: A 54 ILE cc_start: 0.8727 (mm) cc_final: 0.8507 (mt) REVERT: A 94 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: A 96 TYR cc_start: 0.8405 (t80) cc_final: 0.7969 (t80) REVERT: A 118 MET cc_start: 0.8614 (mmp) cc_final: 0.7834 (mmp) REVERT: A 145 ASN cc_start: 0.8888 (t0) cc_final: 0.8668 (t0) REVERT: A 245 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6635 (t0) REVERT: A 255 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7169 (ttp-110) REVERT: A 308 GLN cc_start: 0.7899 (mt0) cc_final: 0.7643 (mt0) REVERT: A 342 ASP cc_start: 0.7506 (t0) cc_final: 0.7178 (t0) REVERT: A 425 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7473 (mtm-85) REVERT: B 63 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 131 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6680 (mm-30) REVERT: B 209 ARG cc_start: 0.7708 (mpt-90) cc_final: 0.7432 (mtt90) REVERT: B 234 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8339 (mptp) REVERT: B 255 PHE cc_start: 0.7600 (m-80) cc_final: 0.6985 (m-80) REVERT: B 401 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: B 549 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7461 (mtt180) REVERT: C 39 GLN cc_start: 0.7807 (tt0) cc_final: 0.7431 (tp40) REVERT: C 82 GLN cc_start: 0.6662 (tp40) cc_final: 0.6258 (tp40) outliers start: 25 outliers final: 4 residues processed: 179 average time/residue: 1.5598 time to fit residues: 296.1414 Evaluate side-chains 155 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 401 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 305 GLN B 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10398 Z= 0.200 Angle : 0.522 8.213 14108 Z= 0.264 Chirality : 0.040 0.175 1606 Planarity : 0.004 0.041 1783 Dihedral : 6.604 88.016 1504 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.05 % Allowed : 14.22 % Favored : 82.73 % 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: 0.11 (0.23), residues: 1275 helix: 0.75 (0.18), residues: 793 sheet: 0.45 (0.48), residues: 115 loop : -1.44 (0.27), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 36 HIS 0.002 0.001 HIS A 87 PHE 0.014 0.001 PHE A 304 TYR 0.014 0.001 TYR A 588 ARG 0.007 0.000 ARG A 594 *********************** 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 191 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7412 (mtt90) cc_final: 0.7065 (ttp-110) REVERT: A 96 TYR cc_start: 0.8420 (t80) cc_final: 0.7983 (t80) REVERT: A 118 MET cc_start: 0.8630 (mmp) cc_final: 0.8189 (mmp) REVERT: A 145 ASN cc_start: 0.8864 (t0) cc_final: 0.8617 (t0) REVERT: A 146 GLN cc_start: 0.7856 (mp-120) cc_final: 0.7586 (mp-120) REVERT: A 245 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6695 (t0) REVERT: A 308 GLN cc_start: 0.7889 (mt0) cc_final: 0.7626 (mt0) REVERT: A 425 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7552 (mtm110) REVERT: B 63 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 181 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7132 (tpp80) REVERT: B 234 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8337 (mptp) REVERT: B 255 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: B 401 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 426 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: B 574 LYS cc_start: 0.7884 (ttpp) cc_final: 0.7602 (pttp) REVERT: C 18 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6397 (tt) REVERT: C 39 GLN cc_start: 0.7926 (tt0) cc_final: 0.7525 (tp40) REVERT: C 82 GLN cc_start: 0.6704 (tp40) cc_final: 0.6269 (tp40) outliers start: 32 outliers final: 8 residues processed: 179 average time/residue: 1.4983 time to fit residues: 284.4979 Evaluate side-chains 162 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10398 Z= 0.380 Angle : 0.618 8.393 14108 Z= 0.312 Chirality : 0.044 0.175 1606 Planarity : 0.004 0.041 1783 Dihedral : 7.318 87.862 1504 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.63 % Allowed : 14.79 % Favored : 81.58 % 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: -0.09 (0.22), residues: 1275 helix: 0.61 (0.18), residues: 787 sheet: 0.16 (0.47), residues: 115 loop : -1.43 (0.27), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 36 HIS 0.004 0.001 HIS B 556 PHE 0.020 0.002 PHE A 568 TYR 0.021 0.002 TYR B 464 ARG 0.009 0.001 ARG B 218 *********************** 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 198 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7844 (mt) cc_final: 0.7459 (tt) REVERT: A 20 ARG cc_start: 0.7358 (mtt90) cc_final: 0.6989 (ttp-110) REVERT: A 145 ASN cc_start: 0.8911 (t0) cc_final: 0.8700 (t0) REVERT: A 232 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: A 244 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6822 (mtp85) REVERT: A 245 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6899 (t0) REVERT: A 255 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7287 (ttp-110) REVERT: A 308 GLN cc_start: 0.7978 (mt0) cc_final: 0.7539 (mt0) REVERT: A 334 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: A 425 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7564 (mtm110) REVERT: B 63 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8218 (tp) REVERT: B 181 ARG cc_start: 0.7363 (mtm110) cc_final: 0.7070 (tpp80) REVERT: B 209 ARG cc_start: 0.7832 (mpt-90) cc_final: 0.7597 (mtt90) REVERT: B 255 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: B 349 ASP cc_start: 0.7439 (t70) cc_final: 0.7218 (t0) REVERT: B 401 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: B 426 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: B 574 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7649 (pttp) REVERT: C 39 GLN cc_start: 0.7956 (tt0) cc_final: 0.7569 (tp40) REVERT: C 82 GLN cc_start: 0.6684 (tp40) cc_final: 0.6258 (tp40) outliers start: 38 outliers final: 17 residues processed: 179 average time/residue: 1.4823 time to fit residues: 282.0276 Evaluate side-chains 172 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 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 305 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10398 Z= 0.215 Angle : 0.535 8.596 14108 Z= 0.272 Chirality : 0.040 0.175 1606 Planarity : 0.004 0.039 1783 Dihedral : 6.846 89.900 1504 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 15.84 % Favored : 81.58 % 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: 0.20 (0.23), residues: 1275 helix: 0.87 (0.18), residues: 793 sheet: 0.20 (0.47), residues: 116 loop : -1.41 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 36 HIS 0.003 0.001 HIS B 556 PHE 0.020 0.001 PHE B 178 TYR 0.011 0.001 TYR B 464 ARG 0.007 0.000 ARG B 218 *********************** 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 180 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7343 (mtt90) cc_final: 0.6983 (ttp-110) REVERT: A 145 ASN cc_start: 0.8875 (t0) cc_final: 0.8651 (t0) REVERT: A 224 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 245 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6751 (t0) REVERT: A 308 GLN cc_start: 0.7848 (mt0) cc_final: 0.7544 (mt0) REVERT: A 342 ASP cc_start: 0.7556 (t0) cc_final: 0.7276 (t0) REVERT: A 425 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7574 (mtm110) REVERT: B 63 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8188 (tp) REVERT: B 119 MET cc_start: 0.8157 (mmm) cc_final: 0.7637 (mmm) REVERT: B 181 ARG cc_start: 0.7349 (mtm110) cc_final: 0.7075 (tpp80) REVERT: B 209 ARG cc_start: 0.7825 (mpt-90) cc_final: 0.7609 (mtt90) REVERT: B 255 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: B 401 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: B 426 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: B 549 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7303 (mtt180) REVERT: B 557 GLU cc_start: 0.7652 (mp0) cc_final: 0.7371 (mp0) REVERT: B 574 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7665 (pttp) REVERT: C 39 GLN cc_start: 0.7928 (tt0) cc_final: 0.7556 (tp40) REVERT: C 82 GLN cc_start: 0.6705 (tp40) cc_final: 0.6315 (tp40) outliers start: 27 outliers final: 10 residues processed: 169 average time/residue: 1.5216 time to fit residues: 272.7299 Evaluate side-chains 160 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 chunk 89 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 305 GLN A 537 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10398 Z= 0.155 Angle : 0.513 8.769 14108 Z= 0.260 Chirality : 0.038 0.170 1606 Planarity : 0.004 0.038 1783 Dihedral : 6.563 88.694 1504 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.58 % Allowed : 16.13 % Favored : 81.30 % 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: 0.54 (0.23), residues: 1275 helix: 1.17 (0.19), residues: 785 sheet: 0.09 (0.46), residues: 121 loop : -1.24 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 36 HIS 0.002 0.000 HIS B 556 PHE 0.021 0.001 PHE A 171 TYR 0.012 0.001 TYR B 164 ARG 0.006 0.000 ARG B 532 *********************** 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 189 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7367 (mtt90) cc_final: 0.7017 (ttp-110) REVERT: A 145 ASN cc_start: 0.8849 (t0) cc_final: 0.8607 (t0) REVERT: A 224 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 238 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8338 (ttmm) REVERT: A 245 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6761 (t0) REVERT: A 255 ARG cc_start: 0.7412 (ttm-80) cc_final: 0.7164 (ttp-110) REVERT: A 308 GLN cc_start: 0.7811 (mt0) cc_final: 0.7498 (mt0) REVERT: A 336 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 342 ASP cc_start: 0.7557 (t0) cc_final: 0.7280 (t0) REVERT: A 425 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7575 (mtm110) REVERT: B 63 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (tp) REVERT: B 181 ARG cc_start: 0.7271 (mtm110) cc_final: 0.7047 (tpp80) REVERT: B 255 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: B 401 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: B 426 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: B 528 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7984 (tp) REVERT: B 549 ARG cc_start: 0.7704 (mtt-85) cc_final: 0.7333 (mtt180) REVERT: B 557 GLU cc_start: 0.7653 (mp0) cc_final: 0.7389 (mp0) REVERT: B 574 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7598 (pttp) REVERT: C 39 GLN cc_start: 0.7920 (tt0) cc_final: 0.7545 (tp40) REVERT: C 82 GLN cc_start: 0.6736 (tp40) cc_final: 0.6232 (tp40) outliers start: 27 outliers final: 7 residues processed: 176 average time/residue: 1.4990 time to fit residues: 280.2536 Evaluate side-chains 173 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 537 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10398 Z= 0.189 Angle : 0.533 8.909 14108 Z= 0.266 Chirality : 0.039 0.174 1606 Planarity : 0.004 0.037 1783 Dihedral : 6.579 88.313 1504 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.39 % Allowed : 16.79 % Favored : 80.82 % 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: 0.63 (0.23), residues: 1275 helix: 1.26 (0.19), residues: 786 sheet: 0.01 (0.46), residues: 121 loop : -1.21 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 36 HIS 0.002 0.001 HIS B 531 PHE 0.017 0.001 PHE B 178 TYR 0.010 0.001 TYR B 164 ARG 0.010 0.000 ARG B 209 *********************** 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 186 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7342 (mtt90) cc_final: 0.6992 (ttp-110) REVERT: A 118 MET cc_start: 0.8588 (mmp) cc_final: 0.7814 (mmp) REVERT: A 134 MET cc_start: 0.7877 (mmm) cc_final: 0.7543 (mmm) REVERT: A 145 ASN cc_start: 0.8861 (t0) cc_final: 0.8620 (t0) REVERT: A 224 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 238 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8244 (mttm) REVERT: A 245 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.6837 (t0) REVERT: A 255 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.7237 (ttp-110) REVERT: A 308 GLN cc_start: 0.7793 (mt0) cc_final: 0.7505 (mt0) REVERT: A 342 ASP cc_start: 0.7567 (t0) cc_final: 0.7271 (t0) REVERT: A 425 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7591 (mtm110) REVERT: B 63 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8181 (tp) REVERT: B 138 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 255 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: B 401 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: B 426 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: B 549 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7355 (mtt180) REVERT: B 557 GLU cc_start: 0.7671 (mp0) cc_final: 0.7390 (mp0) REVERT: B 574 LYS cc_start: 0.7860 (ttpp) cc_final: 0.7588 (pttp) REVERT: C 39 GLN cc_start: 0.7927 (tt0) cc_final: 0.7557 (tp40) REVERT: C 82 GLN cc_start: 0.6675 (tp40) cc_final: 0.6165 (tp40) outliers start: 25 outliers final: 11 residues processed: 174 average time/residue: 1.5245 time to fit residues: 281.9881 Evaluate side-chains 175 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 107 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 429 GLN A 537 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10398 Z= 0.186 Angle : 0.538 9.005 14108 Z= 0.269 Chirality : 0.039 0.175 1606 Planarity : 0.004 0.052 1783 Dihedral : 6.553 88.363 1504 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.39 % Allowed : 16.70 % Favored : 80.92 % 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: 0.68 (0.23), residues: 1275 helix: 1.31 (0.19), residues: 786 sheet: 0.01 (0.46), residues: 121 loop : -1.19 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 36 HIS 0.001 0.000 HIS A 87 PHE 0.029 0.001 PHE A 171 TYR 0.019 0.001 TYR B 164 ARG 0.012 0.000 ARG A 233 *********************** 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 183 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7339 (mtt90) cc_final: 0.6991 (ttp-110) REVERT: A 118 MET cc_start: 0.8589 (mmp) cc_final: 0.7793 (mmp) REVERT: A 134 MET cc_start: 0.7854 (mmm) cc_final: 0.7409 (mmm) REVERT: A 145 ASN cc_start: 0.8852 (t0) cc_final: 0.8606 (t0) REVERT: A 166 LEU cc_start: 0.7661 (tp) cc_final: 0.7456 (tm) REVERT: A 224 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: A 238 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8262 (mttm) REVERT: A 245 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6824 (t0) REVERT: A 255 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.7219 (ttp-110) REVERT: A 308 GLN cc_start: 0.7826 (mt0) cc_final: 0.7512 (mt0) REVERT: A 342 ASP cc_start: 0.7556 (t0) cc_final: 0.7283 (t0) REVERT: A 425 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7587 (mtm110) REVERT: B 63 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 138 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8554 (mt) REVERT: B 255 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: B 401 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: B 412 LYS cc_start: 0.8591 (mptp) cc_final: 0.8360 (mmtt) REVERT: B 426 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: B 549 ARG cc_start: 0.7712 (mtt-85) cc_final: 0.7352 (mtt180) REVERT: B 557 GLU cc_start: 0.7669 (mp0) cc_final: 0.7397 (mp0) REVERT: B 574 LYS cc_start: 0.7817 (ttpp) cc_final: 0.7534 (pttp) REVERT: C 39 GLN cc_start: 0.7934 (tt0) cc_final: 0.7575 (tp40) REVERT: C 82 GLN cc_start: 0.6690 (tp40) cc_final: 0.6174 (tp40) outliers start: 25 outliers final: 11 residues processed: 173 average time/residue: 1.5055 time to fit residues: 277.6602 Evaluate side-chains 178 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.3980 chunk 120 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 537 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10398 Z= 0.187 Angle : 0.540 9.117 14108 Z= 0.271 Chirality : 0.039 0.173 1606 Planarity : 0.004 0.059 1783 Dihedral : 6.534 88.176 1504 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.19 % Allowed : 16.89 % Favored : 80.92 % 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: 0.73 (0.23), residues: 1275 helix: 1.34 (0.19), residues: 786 sheet: 0.02 (0.46), residues: 121 loop : -1.17 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 36 HIS 0.002 0.001 HIS A 121 PHE 0.016 0.001 PHE B 178 TYR 0.019 0.001 TYR B 164 ARG 0.013 0.000 ARG A 233 ********************** 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 181 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7338 (mtt90) cc_final: 0.6989 (ttp-110) REVERT: A 118 MET cc_start: 0.8573 (mmp) cc_final: 0.7796 (mmp) REVERT: A 134 MET cc_start: 0.7889 (mmm) cc_final: 0.7429 (mmm) REVERT: A 145 ASN cc_start: 0.8846 (t0) cc_final: 0.8607 (t0) REVERT: A 166 LEU cc_start: 0.7676 (tp) cc_final: 0.7474 (tm) REVERT: A 224 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 238 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8263 (mttm) REVERT: A 245 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6789 (t0) REVERT: A 255 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7215 (ttp-110) REVERT: A 308 GLN cc_start: 0.7741 (mt0) cc_final: 0.7451 (mt0) REVERT: A 334 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7136 (tt0) REVERT: A 342 ASP cc_start: 0.7570 (t0) cc_final: 0.7304 (t0) REVERT: A 425 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7591 (mtm110) REVERT: B 63 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 138 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8539 (mt) REVERT: B 255 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: B 401 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: B 426 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: B 549 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7355 (mtt180) REVERT: B 557 GLU cc_start: 0.7668 (mp0) cc_final: 0.7398 (mp0) REVERT: B 574 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7533 (pttp) REVERT: C 39 GLN cc_start: 0.7932 (tt0) cc_final: 0.7575 (tp40) REVERT: C 82 GLN cc_start: 0.6687 (tp40) cc_final: 0.6191 (tp40) outliers start: 23 outliers final: 12 residues processed: 173 average time/residue: 1.4929 time to fit residues: 275.1914 Evaluate side-chains 168 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110619 restraints weight = 11716.008| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.77 r_work: 0.3094 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10398 Z= 0.204 Angle : 0.550 9.174 14108 Z= 0.276 Chirality : 0.040 0.190 1606 Planarity : 0.004 0.058 1783 Dihedral : 6.623 88.488 1504 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.19 % Allowed : 17.08 % Favored : 80.73 % 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: 0.68 (0.23), residues: 1275 helix: 1.29 (0.18), residues: 792 sheet: -0.01 (0.46), residues: 121 loop : -1.18 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 36 HIS 0.002 0.001 HIS B 531 PHE 0.029 0.001 PHE A 171 TYR 0.018 0.001 TYR B 164 ARG 0.012 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4880.02 seconds wall clock time: 86 minutes 50.38 seconds (5210.38 seconds total)