Starting phenix.real_space_refine on Mon Jul 28 14:36:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ram_4780/07_2025/6ram_4780.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ram_4780/07_2025/6ram_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/cci-nas-00/data/ceres_data/6ram_4780/07_2025/6ram_4780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ram_4780/07_2025/6ram_4780.map" model { file = "/net/cci-nas-00/data/ceres_data/6ram_4780/07_2025/6ram_4780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ram_4780/07_2025/6ram_4780.cif" } 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. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.46, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 57 helices and 8 sheets defined 64.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 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) Processing helix chain 'A' and resid 21 through 28 Proline residue: A 24 - end of helix removed outlier: 4.927A pdb=" N LEU A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 45 removed outlier: 3.654A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 72 through 120 removed outlier: 3.705A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.526A pdb=" N LEU A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) 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 138 through 155 removed outlier: 3.529A pdb=" N THR A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.905A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.871A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.529A pdb=" N LEU A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 221 removed outlier: 4.457A pdb=" N GLU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 233 through 285 removed outlier: 3.577A pdb=" N GLU A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) 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) removed outlier: 3.841A pdb=" N ARG A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 313 through 332 removed outlier: 3.822A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 removed outlier: 3.704A pdb=" N VAL A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) 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 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.673A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.874A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 484 through 487 removed outlier: 3.656A pdb=" N GLN A 487 " --> pdb=" O LYS A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.690A pdb=" N GLY A 494 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 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 529 through 544 removed outlier: 3.928A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.914A pdb=" N ILE A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 598 removed outlier: 3.758A pdb=" N ALA A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.684A pdb=" N TRP B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.651A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 103 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 106 through 113 removed outlier: 4.225A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 removed outlier: 3.552A pdb=" N LEU B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 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) removed outlier: 3.976A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.983A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 207 removed outlier: 4.188A pdb=" N GLY B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) 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 207 through 214 Processing helix chain 'B' and resid 217 through 270 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 274 through 317 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) removed outlier: 3.543A pdb=" N ASP B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.797A pdb=" N LEU B 335 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.602A pdb=" N LEU B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.568A pdb=" N ARG B 404 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 440 through 451 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 453 through 460 Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.731A pdb=" N GLU B 465 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 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 506 through 520 Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.788A pdb=" N LEU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.511A pdb=" N GLN B 561 " --> pdb=" O SER B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 removed outlier: 3.751A pdb=" N LEU B 572 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379 removed outlier: 6.144A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 353 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 379 removed outlier: 6.144A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 416 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A 358 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ARG A 414 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.308A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 577 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 449 removed outlier: 3.532A pdb=" N GLY A 448 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.434A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 343 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 392 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.496A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 541 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 552 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP B 546 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA7, 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=AA8, first strand: chain 'C' and resid 11 through 12 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) 577 hydrogen bonds defined for protein. 1692 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: 3.49 Time building geometry restraints manager: 2.72 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: 0.00 - 4.78: 13684 4.78 - 9.55: 406 9.55 - 14.33: 16 14.33 - 19.11: 0 19.11 - 23.88: 2 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: 459 2.71 - 3.26: 10007 3.26 - 3.80: 15369 3.80 - 4.35: 20680 4.35 - 4.90: 33370 Nonbonded interactions: 79885 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 79880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.370 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.970 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- 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 10401 Z= 1.142 Angle : 1.964 23.885 14112 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 Details of bonding type rmsd hydrogen bonds : bond 0.24935 ( 575) hydrogen bonds : angle 8.57617 ( 1692) SS BOND : bond 0.02220 ( 2) SS BOND : angle 2.01736 ( 4) covalent geometry : bond 0.01648 (10399) covalent geometry : angle 1.96419 (14108) *********************** 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 to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 1.064 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: 0.3013 time to fit residues: 127.9434 Evaluate side-chains 198 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079821 restraints weight = 25689.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082622 restraints weight = 13668.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084553 restraints weight = 8885.005| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10401 Z= 0.170 Angle : 0.711 10.056 14112 Z= 0.362 Chirality : 0.042 0.182 1607 Planarity : 0.005 0.056 1784 Dihedral : 6.613 63.066 1485 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.43 % Allowed : 11.44 % Favored : 85.13 % 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: -1.16 (0.22), residues: 1275 helix: -0.39 (0.18), residues: 768 sheet: -0.39 (0.43), residues: 130 loop : -1.40 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 290 HIS 0.006 0.002 HIS B 454 PHE 0.023 0.002 PHE A 88 TYR 0.017 0.002 TYR A 589 ARG 0.011 0.001 ARG A 569 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 575) hydrogen bonds : angle 4.77894 ( 1692) SS BOND : bond 0.00913 ( 2) SS BOND : angle 1.19144 ( 4) covalent geometry : bond 0.00355 (10399) covalent geometry : angle 0.71044 (14108) *********************** 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 261 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9243 (mt) cc_final: 0.8790 (tt) REVERT: A 40 THR cc_start: 0.9200 (m) cc_final: 0.8882 (p) REVERT: A 94 GLU cc_start: 0.7996 (tp30) cc_final: 0.7631 (tp30) REVERT: A 118 MET cc_start: 0.9058 (mmp) cc_final: 0.8495 (mmp) REVERT: A 305 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: A 309 ASP cc_start: 0.8304 (t0) cc_final: 0.7980 (t0) REVERT: A 359 TRP cc_start: 0.7998 (m100) cc_final: 0.7405 (m100) REVERT: A 365 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8366 (ttmt) REVERT: A 376 LEU cc_start: 0.8300 (mp) cc_final: 0.8052 (mm) REVERT: A 444 PHE cc_start: 0.7242 (t80) cc_final: 0.6085 (t80) REVERT: A 569 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7279 (mtt90) REVERT: B 21 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7802 (ptt90) REVERT: B 38 PHE cc_start: 0.8714 (t80) cc_final: 0.8501 (t80) REVERT: B 132 MET cc_start: 0.8949 (tmm) cc_final: 0.8688 (tmm) REVERT: B 255 PHE cc_start: 0.8728 (t80) cc_final: 0.8308 (t80) REVERT: B 281 PHE cc_start: 0.9050 (t80) cc_final: 0.8402 (t80) REVERT: B 282 ASN cc_start: 0.8982 (t0) cc_final: 0.8766 (t0) REVERT: B 299 MET cc_start: 0.8775 (mmm) cc_final: 0.8474 (mmp) REVERT: B 301 LEU cc_start: 0.8584 (tt) cc_final: 0.8322 (tp) REVERT: B 316 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8429 (mt) REVERT: B 505 VAL cc_start: 0.9067 (t) cc_final: 0.8854 (p) REVERT: C 20 LEU cc_start: 0.8771 (tp) cc_final: 0.8353 (tp) REVERT: C 46 GLU cc_start: 0.7810 (pm20) cc_final: 0.7586 (pm20) REVERT: C 51 ILE cc_start: 0.8888 (tp) cc_final: 0.8644 (tp) REVERT: C 65 LYS cc_start: 0.9032 (pttp) cc_final: 0.8687 (pttm) REVERT: C 84 ASN cc_start: 0.8636 (m-40) cc_final: 0.7998 (p0) REVERT: C 86 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8254 (mt) outliers start: 36 outliers final: 14 residues processed: 245 average time/residue: 0.2404 time to fit residues: 80.5424 Evaluate side-chains 185 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 180 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 VAL 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 86 LEU 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 83 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN C 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.097698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.078735 restraints weight = 25738.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081487 restraints weight = 13656.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083387 restraints weight = 8881.248| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10401 Z= 0.134 Angle : 0.663 8.490 14112 Z= 0.326 Chirality : 0.041 0.223 1607 Planarity : 0.004 0.039 1784 Dihedral : 5.822 52.665 1481 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.48 % Allowed : 14.68 % Favored : 82.84 % 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: -0.42 (0.22), residues: 1275 helix: 0.29 (0.18), residues: 773 sheet: -0.40 (0.43), residues: 126 loop : -1.21 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 290 HIS 0.008 0.001 HIS C 80 PHE 0.020 0.001 PHE A 317 TYR 0.024 0.001 TYR B 92 ARG 0.008 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 575) hydrogen bonds : angle 4.33955 ( 1692) SS BOND : bond 0.00126 ( 2) SS BOND : angle 1.77133 ( 4) covalent geometry : bond 0.00292 (10399) covalent geometry : angle 0.66253 (14108) *********************** 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 215 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.194 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: 0.9197 (m) cc_final: 0.8923 (p) REVERT: A 72 LEU cc_start: 0.7822 (mm) cc_final: 0.7518 (mm) REVERT: A 94 GLU cc_start: 0.8107 (tp30) cc_final: 0.7849 (tp30) REVERT: A 140 ASP cc_start: 0.6850 (m-30) cc_final: 0.6253 (m-30) REVERT: A 145 ASN cc_start: 0.8638 (m-40) cc_final: 0.8083 (m110) REVERT: A 152 LEU cc_start: 0.8370 (mt) cc_final: 0.7684 (mt) REVERT: A 359 TRP cc_start: 0.8152 (m100) cc_final: 0.7283 (m100) REVERT: A 376 LEU cc_start: 0.8312 (mp) cc_final: 0.8014 (mm) REVERT: A 417 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 132 MET cc_start: 0.8989 (tmm) cc_final: 0.8727 (tmm) REVERT: B 255 PHE cc_start: 0.8698 (t80) cc_final: 0.8261 (t80) REVERT: B 281 PHE cc_start: 0.8982 (t80) cc_final: 0.8712 (t80) REVERT: B 282 ASN cc_start: 0.9040 (t0) cc_final: 0.8746 (t0) REVERT: B 365 MET cc_start: 0.8439 (tmm) cc_final: 0.8156 (tmm) REVERT: B 505 VAL cc_start: 0.8923 (t) cc_final: 0.8690 (p) REVERT: C 20 LEU cc_start: 0.8838 (tp) cc_final: 0.8297 (tp) REVERT: C 45 ARG cc_start: 0.8292 (mtm110) cc_final: 0.7956 (mtm110) REVERT: C 52 SER cc_start: 0.8554 (t) cc_final: 0.8329 (p) REVERT: C 65 LYS cc_start: 0.9048 (pttp) cc_final: 0.8689 (pttm) outliers start: 26 outliers final: 14 residues processed: 209 average time/residue: 0.2479 time to fit residues: 70.9993 Evaluate side-chains 176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 165 LEU 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 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 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 63 SER 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 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 120 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078476 restraints weight = 25582.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081294 restraints weight = 13536.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083223 restraints weight = 8807.195| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10401 Z= 0.122 Angle : 0.634 8.102 14112 Z= 0.306 Chirality : 0.040 0.168 1607 Planarity : 0.004 0.048 1784 Dihedral : 5.519 56.879 1481 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.05 % Allowed : 16.59 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1275 helix: 0.72 (0.19), residues: 773 sheet: -0.25 (0.44), residues: 125 loop : -1.25 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 446 HIS 0.004 0.001 HIS C 80 PHE 0.036 0.001 PHE A 15 TYR 0.019 0.001 TYR B 92 ARG 0.009 0.001 ARG A 569 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 575) hydrogen bonds : angle 4.18358 ( 1692) SS BOND : bond 0.01614 ( 2) SS BOND : angle 1.56329 ( 4) covalent geometry : bond 0.00267 (10399) covalent geometry : angle 0.63343 (14108) *********************** 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 214 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9202 (m) cc_final: 0.8921 (p) REVERT: A 72 LEU cc_start: 0.7816 (mm) cc_final: 0.7543 (mm) REVERT: A 94 GLU cc_start: 0.8132 (tp30) cc_final: 0.7850 (tp30) REVERT: A 140 ASP cc_start: 0.6674 (m-30) cc_final: 0.6181 (m-30) REVERT: A 145 ASN cc_start: 0.8620 (m-40) cc_final: 0.8004 (m110) REVERT: A 331 LEU cc_start: 0.8490 (tt) cc_final: 0.8167 (tt) REVERT: A 359 TRP cc_start: 0.8074 (m100) cc_final: 0.7271 (m100) REVERT: A 365 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7979 (ttmt) REVERT: A 376 LEU cc_start: 0.8330 (mp) cc_final: 0.8050 (mm) REVERT: A 391 LEU cc_start: 0.8988 (mp) cc_final: 0.8694 (mt) REVERT: A 417 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 112 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8245 (mttp) REVERT: B 132 MET cc_start: 0.9042 (tmm) cc_final: 0.8702 (tmm) REVERT: B 154 MET cc_start: 0.8578 (mmm) cc_final: 0.7862 (mmm) REVERT: B 282 ASN cc_start: 0.9000 (t0) cc_final: 0.8653 (t0) REVERT: B 319 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8428 (mmmt) REVERT: B 489 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8872 (tt) REVERT: B 505 VAL cc_start: 0.8879 (t) cc_final: 0.8656 (p) REVERT: C 13 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7172 (tp40) REVERT: C 45 ARG cc_start: 0.8372 (mtm110) cc_final: 0.8001 (mtm110) REVERT: C 76 LYS cc_start: 0.9012 (tppt) cc_final: 0.8737 (tptp) REVERT: C 107 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7263 (tpt-90) outliers start: 32 outliers final: 15 residues processed: 202 average time/residue: 0.2418 time to fit residues: 67.7070 Evaluate side-chains 177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 305 GLN 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 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 344 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 528 LEU 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 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 280 GLN B 419 GLN B 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076973 restraints weight = 25493.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079727 restraints weight = 13625.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081625 restraints weight = 8904.561| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10401 Z= 0.140 Angle : 0.625 8.523 14112 Z= 0.303 Chirality : 0.040 0.154 1607 Planarity : 0.004 0.057 1784 Dihedral : 5.344 57.557 1481 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.15 % Allowed : 17.92 % Favored : 78.93 % 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: 0.27 (0.23), residues: 1275 helix: 0.89 (0.19), residues: 781 sheet: -0.13 (0.45), residues: 125 loop : -1.09 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.006 0.001 HIS A 561 PHE 0.030 0.001 PHE A 15 TYR 0.019 0.001 TYR B 92 ARG 0.006 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 575) hydrogen bonds : angle 4.14245 ( 1692) SS BOND : bond 0.00472 ( 2) SS BOND : angle 1.42640 ( 4) covalent geometry : bond 0.00313 (10399) covalent geometry : angle 0.62473 (14108) *********************** 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 209 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9255 (m) cc_final: 0.8987 (p) REVERT: A 94 GLU cc_start: 0.8147 (tp30) cc_final: 0.7682 (tp30) REVERT: A 140 ASP cc_start: 0.6831 (m-30) cc_final: 0.6366 (m-30) REVERT: A 145 ASN cc_start: 0.8627 (m-40) cc_final: 0.7961 (m110) REVERT: A 238 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7832 (tmtt) REVERT: A 359 TRP cc_start: 0.8110 (m100) cc_final: 0.7317 (m100) REVERT: A 376 LEU cc_start: 0.8456 (mp) cc_final: 0.8093 (mt) REVERT: A 391 LEU cc_start: 0.9007 (mp) cc_final: 0.8713 (mt) REVERT: A 417 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 441 GLN cc_start: 0.8043 (tt0) cc_final: 0.7632 (tp-100) REVERT: B 132 MET cc_start: 0.9116 (tmm) cc_final: 0.8477 (tmm) REVERT: B 154 MET cc_start: 0.8646 (mmm) cc_final: 0.7981 (mmm) REVERT: B 188 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8732 (tpp80) REVERT: B 365 MET cc_start: 0.8434 (tmm) cc_final: 0.8143 (tmm) REVERT: B 505 VAL cc_start: 0.8889 (t) cc_final: 0.8642 (p) REVERT: C 20 LEU cc_start: 0.8581 (tp) cc_final: 0.8302 (tp) REVERT: C 45 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8045 (mtm110) REVERT: C 65 LYS cc_start: 0.9003 (pttp) cc_final: 0.8713 (pttm) REVERT: C 76 LYS cc_start: 0.8995 (tppt) cc_final: 0.8749 (tptp) REVERT: C 107 ARG cc_start: 0.7470 (mmm160) cc_final: 0.6878 (ttt-90) outliers start: 33 outliers final: 22 residues processed: 193 average time/residue: 0.2472 time to fit residues: 65.1086 Evaluate side-chains 176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 165 LEU Chi-restraints excluded: chain A residue 188 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 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 PHE 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 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 63 SER 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 45 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077204 restraints weight = 25771.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.079990 restraints weight = 13660.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081879 restraints weight = 8905.516| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10401 Z= 0.130 Angle : 0.624 7.654 14112 Z= 0.303 Chirality : 0.040 0.154 1607 Planarity : 0.004 0.047 1784 Dihedral : 5.199 60.287 1481 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.34 % Allowed : 18.59 % Favored : 78.07 % 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: 0.52 (0.23), residues: 1275 helix: 1.09 (0.19), residues: 781 sheet: 0.18 (0.45), residues: 132 loop : -1.12 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 290 HIS 0.004 0.001 HIS A 561 PHE 0.027 0.001 PHE A 15 TYR 0.016 0.001 TYR B 92 ARG 0.006 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 575) hydrogen bonds : angle 4.07995 ( 1692) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.18695 ( 4) covalent geometry : bond 0.00294 (10399) covalent geometry : angle 0.62361 (14108) *********************** 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 201 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.200 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: 0.9269 (m) cc_final: 0.9004 (p) REVERT: A 140 ASP cc_start: 0.6819 (m-30) cc_final: 0.6305 (m-30) REVERT: A 145 ASN cc_start: 0.8612 (m-40) cc_final: 0.7919 (m110) REVERT: A 238 LYS cc_start: 0.8056 (tmtt) cc_final: 0.7837 (tmtt) REVERT: A 391 LEU cc_start: 0.8981 (mp) cc_final: 0.8666 (mt) REVERT: A 417 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8673 (p) REVERT: A 441 GLN cc_start: 0.7944 (tt0) cc_final: 0.7619 (tp-100) REVERT: B 112 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8161 (mttp) REVERT: B 132 MET cc_start: 0.9134 (tmm) cc_final: 0.8492 (tmm) REVERT: B 154 MET cc_start: 0.8626 (mmm) cc_final: 0.7941 (mmm) REVERT: B 188 ARG cc_start: 0.9086 (mmm-85) cc_final: 0.8794 (tpp80) REVERT: B 281 PHE cc_start: 0.8856 (t80) cc_final: 0.7226 (t80) REVERT: B 365 MET cc_start: 0.8341 (tmm) cc_final: 0.8099 (tmm) REVERT: B 505 VAL cc_start: 0.8908 (t) cc_final: 0.8657 (p) REVERT: C 65 LYS cc_start: 0.9002 (pttp) cc_final: 0.8657 (pttm) REVERT: C 83 MET cc_start: 0.8991 (mpp) cc_final: 0.8697 (mpp) REVERT: C 107 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6880 (ttt-90) outliers start: 35 outliers final: 20 residues processed: 189 average time/residue: 0.2149 time to fit residues: 58.1634 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 245 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 310 LEU 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 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 176 MET 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 528 LEU Chi-restraints excluded: chain B residue 569 MET 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 93 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077282 restraints weight = 25999.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.080097 restraints weight = 13692.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082004 restraints weight = 8892.967| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10401 Z= 0.135 Angle : 0.647 9.265 14112 Z= 0.313 Chirality : 0.040 0.186 1607 Planarity : 0.004 0.043 1784 Dihedral : 5.146 61.753 1481 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.24 % Allowed : 19.35 % 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: 0.62 (0.23), residues: 1275 helix: 1.16 (0.19), residues: 784 sheet: 0.25 (0.45), residues: 133 loop : -1.10 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 PHE 0.017 0.001 PHE A 317 TYR 0.027 0.001 TYR C 113 ARG 0.006 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 575) hydrogen bonds : angle 4.10760 ( 1692) SS BOND : bond 0.00115 ( 2) SS BOND : angle 1.28459 ( 4) covalent geometry : bond 0.00306 (10399) covalent geometry : angle 0.64712 (14108) *********************** 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 199 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9285 (m) cc_final: 0.9025 (p) REVERT: A 140 ASP cc_start: 0.7081 (m-30) cc_final: 0.6582 (m-30) REVERT: A 238 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7864 (tmtt) REVERT: A 326 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: A 391 LEU cc_start: 0.8989 (mp) cc_final: 0.8666 (mt) REVERT: A 441 GLN cc_start: 0.7978 (tt0) cc_final: 0.7624 (tp-100) REVERT: B 112 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8215 (mttp) REVERT: B 132 MET cc_start: 0.9155 (tmm) cc_final: 0.8503 (tmm) REVERT: B 154 MET cc_start: 0.8682 (mmm) cc_final: 0.8227 (mmm) REVERT: B 188 ARG cc_start: 0.9090 (mmm-85) cc_final: 0.8761 (tpp80) REVERT: B 365 MET cc_start: 0.8297 (tmm) cc_final: 0.8039 (tmm) REVERT: B 505 VAL cc_start: 0.8906 (t) cc_final: 0.8630 (p) REVERT: C 65 LYS cc_start: 0.9005 (pttp) cc_final: 0.8663 (pttm) REVERT: C 76 LYS cc_start: 0.8985 (tppt) cc_final: 0.8724 (tptp) REVERT: C 83 MET cc_start: 0.8988 (mpp) cc_final: 0.8697 (mpp) outliers start: 34 outliers final: 26 residues processed: 184 average time/residue: 0.2294 time to fit residues: 58.8343 Evaluate side-chains 181 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 353 VAL 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 A residue 597 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 MET 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 528 LEU Chi-restraints excluded: chain B residue 569 MET 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 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.077433 restraints weight = 26012.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080224 restraints weight = 13721.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082116 restraints weight = 8934.774| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10401 Z= 0.125 Angle : 0.647 10.549 14112 Z= 0.308 Chirality : 0.040 0.156 1607 Planarity : 0.004 0.051 1784 Dihedral : 5.069 63.829 1481 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.48 % Allowed : 19.83 % Favored : 77.69 % 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: 0.72 (0.23), residues: 1275 helix: 1.25 (0.19), residues: 783 sheet: 0.29 (0.45), residues: 133 loop : -1.08 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 262 HIS 0.003 0.001 HIS B 454 PHE 0.036 0.001 PHE B 38 TYR 0.020 0.001 TYR B 92 ARG 0.006 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 575) hydrogen bonds : angle 4.01174 ( 1692) SS BOND : bond 0.00122 ( 2) SS BOND : angle 1.28002 ( 4) covalent geometry : bond 0.00282 (10399) covalent geometry : angle 0.64686 (14108) *********************** 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 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7016 (m-30) cc_final: 0.6555 (m-30) REVERT: A 238 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7830 (tmtt) REVERT: A 391 LEU cc_start: 0.9008 (mp) cc_final: 0.8715 (mt) REVERT: A 441 GLN cc_start: 0.7944 (tt0) cc_final: 0.7633 (tp-100) REVERT: A 508 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 112 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8197 (mttp) REVERT: B 120 ASN cc_start: 0.8115 (m-40) cc_final: 0.7913 (m110) REVERT: B 132 MET cc_start: 0.9131 (tmm) cc_final: 0.8500 (tmm) REVERT: B 154 MET cc_start: 0.8640 (mmm) cc_final: 0.8050 (mmm) REVERT: B 188 ARG cc_start: 0.9070 (mmm-85) cc_final: 0.8782 (tpp80) REVERT: B 281 PHE cc_start: 0.8729 (t80) cc_final: 0.7491 (t80) REVERT: B 282 ASN cc_start: 0.8874 (t0) cc_final: 0.8486 (t0) REVERT: B 365 MET cc_start: 0.8370 (tmm) cc_final: 0.8161 (tmm) REVERT: B 505 VAL cc_start: 0.8872 (t) cc_final: 0.8576 (p) REVERT: C 65 LYS cc_start: 0.8986 (pttp) cc_final: 0.8657 (pttm) REVERT: C 83 MET cc_start: 0.8965 (mpp) cc_final: 0.8689 (mpp) REVERT: C 107 ARG cc_start: 0.7825 (tpt-90) cc_final: 0.7568 (tpt-90) outliers start: 26 outliers final: 20 residues processed: 173 average time/residue: 0.2474 time to fit residues: 60.2687 Evaluate side-chains 173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 353 VAL 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 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 MET 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 528 LEU Chi-restraints excluded: chain C residue 112 LYS 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 93 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077430 restraints weight = 25856.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.080182 restraints weight = 13684.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082068 restraints weight = 8911.063| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10401 Z= 0.128 Angle : 0.649 10.688 14112 Z= 0.309 Chirality : 0.040 0.153 1607 Planarity : 0.004 0.039 1784 Dihedral : 5.060 63.890 1481 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.38 % Allowed : 20.21 % 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: 0.76 (0.23), residues: 1275 helix: 1.30 (0.19), residues: 783 sheet: 0.31 (0.45), residues: 133 loop : -1.12 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 PHE 0.022 0.001 PHE A 70 TYR 0.018 0.001 TYR B 92 ARG 0.006 0.000 ARG C 45 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 575) hydrogen bonds : angle 4.00987 ( 1692) SS BOND : bond 0.00145 ( 2) SS BOND : angle 1.31476 ( 4) covalent geometry : bond 0.00292 (10399) covalent geometry : angle 0.64899 (14108) *********************** 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 178 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7048 (m-30) cc_final: 0.6557 (m-30) REVERT: A 365 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8152 (ptpp) REVERT: A 391 LEU cc_start: 0.9020 (mp) cc_final: 0.8739 (mt) REVERT: A 441 GLN cc_start: 0.7937 (tt0) cc_final: 0.7643 (tp-100) REVERT: A 508 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 112 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8232 (mttp) REVERT: B 132 MET cc_start: 0.9130 (tmm) cc_final: 0.8444 (tmm) REVERT: B 154 MET cc_start: 0.8636 (mmm) cc_final: 0.8013 (mmm) REVERT: B 188 ARG cc_start: 0.9092 (mmm-85) cc_final: 0.8568 (tpp80) REVERT: B 281 PHE cc_start: 0.8722 (t80) cc_final: 0.7553 (t80) REVERT: B 282 ASN cc_start: 0.8862 (t0) cc_final: 0.8478 (t0) REVERT: B 365 MET cc_start: 0.8363 (tmm) cc_final: 0.8134 (tmm) REVERT: B 505 VAL cc_start: 0.8866 (t) cc_final: 0.8560 (p) REVERT: C 65 LYS cc_start: 0.8951 (pttp) cc_final: 0.8640 (pttm) REVERT: C 83 MET cc_start: 0.8974 (mpp) cc_final: 0.8721 (mpp) outliers start: 25 outliers final: 20 residues processed: 167 average time/residue: 0.2398 time to fit residues: 56.2072 Evaluate side-chains 169 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 245 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 353 VAL 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 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 MET 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 528 LEU 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 2 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** B 120 ASN ** B 191 GLN ** 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 = 0.3558 r_free = 0.3558 target = 0.096074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.076760 restraints weight = 25930.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079502 restraints weight = 13839.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081383 restraints weight = 9059.098| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10401 Z= 0.144 Angle : 0.663 11.253 14112 Z= 0.317 Chirality : 0.040 0.152 1607 Planarity : 0.004 0.039 1784 Dihedral : 5.075 63.495 1481 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.38 % Allowed : 20.88 % Favored : 76.74 % 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: 1.27 (0.19), residues: 784 sheet: 0.38 (0.46), residues: 127 loop : -1.16 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.004 0.001 HIS B 454 PHE 0.026 0.001 PHE A 15 TYR 0.020 0.001 TYR B 16 ARG 0.007 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 575) hydrogen bonds : angle 4.04069 ( 1692) SS BOND : bond 0.00189 ( 2) SS BOND : angle 1.34712 ( 4) covalent geometry : bond 0.00329 (10399) covalent geometry : angle 0.66256 (14108) ********************** 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 178 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7039 (m-30) cc_final: 0.6555 (m-30) REVERT: A 365 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8300 (ptpp) REVERT: A 391 LEU cc_start: 0.9013 (mp) cc_final: 0.8739 (mt) REVERT: A 441 GLN cc_start: 0.7967 (tt0) cc_final: 0.7704 (tp-100) REVERT: B 112 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8309 (mttp) REVERT: B 120 ASN cc_start: 0.8119 (m-40) cc_final: 0.7883 (m110) REVERT: B 132 MET cc_start: 0.9134 (tmm) cc_final: 0.8391 (tmm) REVERT: B 154 MET cc_start: 0.8673 (mmm) cc_final: 0.8085 (mmm) REVERT: B 188 ARG cc_start: 0.9017 (mmm-85) cc_final: 0.8759 (tpp80) REVERT: B 281 PHE cc_start: 0.8742 (t80) cc_final: 0.7567 (t80) REVERT: B 282 ASN cc_start: 0.8911 (t0) cc_final: 0.8533 (t0) REVERT: B 365 MET cc_start: 0.8309 (tmm) cc_final: 0.8062 (tmm) REVERT: B 481 GLN cc_start: 0.8732 (mp10) cc_final: 0.8440 (mp10) REVERT: B 505 VAL cc_start: 0.8880 (t) cc_final: 0.8581 (p) REVERT: C 51 ILE cc_start: 0.9110 (tp) cc_final: 0.8519 (mm) REVERT: C 65 LYS cc_start: 0.8959 (pttp) cc_final: 0.8678 (pttm) REVERT: C 83 MET cc_start: 0.8939 (mpp) cc_final: 0.8686 (mpp) REVERT: C 107 ARG cc_start: 0.7755 (tpt-90) cc_final: 0.7480 (tpt-90) outliers start: 25 outliers final: 22 residues processed: 167 average time/residue: 0.2150 time to fit residues: 50.8745 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 353 VAL 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 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 176 MET 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 528 LEU 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 84 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 5 optimal weight: 0.2980 chunk 108 optimal weight: 0.0470 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079135 restraints weight = 25657.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081971 restraints weight = 13420.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083870 restraints weight = 8663.002| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10401 Z= 0.116 Angle : 0.667 11.610 14112 Z= 0.314 Chirality : 0.040 0.148 1607 Planarity : 0.004 0.041 1784 Dihedral : 5.004 67.034 1481 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.10 % Allowed : 21.45 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1275 helix: 1.37 (0.19), residues: 787 sheet: 0.36 (0.46), residues: 128 loop : -1.18 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 262 HIS 0.003 0.001 HIS B 454 PHE 0.035 0.001 PHE B 38 TYR 0.024 0.001 TYR B 92 ARG 0.006 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 575) hydrogen bonds : angle 3.94112 ( 1692) SS BOND : bond 0.00116 ( 2) SS BOND : angle 1.12604 ( 4) covalent geometry : bond 0.00254 (10399) covalent geometry : angle 0.66709 (14108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.42 seconds wall clock time: 56 minutes 44.78 seconds (3404.78 seconds total)