Starting phenix.real_space_refine on Tue Mar 3 23:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxh_21437/03_2026/6vxh_21437.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxh_21437/03_2026/6vxh_21437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vxh_21437/03_2026/6vxh_21437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxh_21437/03_2026/6vxh_21437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxh_21437/03_2026/6vxh_21437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxh_21437/03_2026/6vxh_21437.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5783 2.51 5 N 1457 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8879 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4393 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 3 Chain: "B" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4393 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'CLR': 1, 'STI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.90, per 1000 atoms: 0.21 Number of scatterers: 8879 At special positions: 0 Unit cell: (106.53, 73.6645, 125.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1581 8.00 N 1457 7.00 C 5783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.15 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 323.6 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 51.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.879A pdb=" N SER A 121 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.635A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 166 removed outlier: 3.732A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.595A pdb=" N MET A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 removed outlier: 4.314A pdb=" N LEU A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 247 through 251 removed outlier: 4.162A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.644A pdb=" N PHE A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 294' Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.685A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.565A pdb=" N LEU A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 383 " --> pdb=" O TRP A 379 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 398 removed outlier: 3.605A pdb=" N GLN A 398 " --> pdb=" O SER A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 398' Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.555A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 440 removed outlier: 3.860A pdb=" N VAL A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 removed outlier: 3.782A pdb=" N ALA A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 removed outlier: 3.826A pdb=" N HIS A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 474 removed outlier: 4.103A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.414A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 527 removed outlier: 4.068A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR A 518 " --> pdb=" O MET A 514 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 527 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.626A pdb=" N ILE A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 551 removed outlier: 4.421A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 removed outlier: 3.518A pdb=" N PHE A 571 " --> pdb=" O LEU A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.308A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 622 through 650 removed outlier: 3.610A pdb=" N LEU A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 639 " --> pdb=" O CYS A 635 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 649 " --> pdb=" O TYR A 645 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.762A pdb=" N ASN B 120 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 121 " --> pdb=" O LYS B 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 117 through 121' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.845A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 removed outlier: 4.343A pdb=" N ARG B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 4.424A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 removed outlier: 4.100A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.032A pdb=" N LYS B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.856A pdb=" N ALA B 280 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.525A pdb=" N PHE B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.550A pdb=" N ALA B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 341 through 350 removed outlier: 3.948A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 removed outlier: 3.503A pdb=" N LEU B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 378 " --> pdb=" O CYS B 374 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 383 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 413 removed outlier: 3.803A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 440 removed outlier: 4.457A pdb=" N VAL B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.639A pdb=" N VAL B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 451 through 461 removed outlier: 3.805A pdb=" N HIS B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 474 removed outlier: 3.520A pdb=" N LEU B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.354A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 527 removed outlier: 4.064A pdb=" N MET B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 511 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 514 " --> pdb=" O MET B 510 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR B 518 " --> pdb=" O MET B 514 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 519 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 551 removed outlier: 4.363A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.522A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 571 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 584 removed outlier: 4.157A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 618 removed outlier: 3.713A pdb=" N LEU B 614 " --> pdb=" O GLY B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 650 removed outlier: 3.628A pdb=" N LEU B 626 " --> pdb=" O SER B 622 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.622A pdb=" N ILE A 42 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 67 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR A 44 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N SER A 65 " --> pdb=" O TYR A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 removed outlier: 6.090A pdb=" N GLY A 74 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 71 removed outlier: 3.566A pdb=" N HIS B 40 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 206 through 208 266 hydrogen bonds defined for protein. 753 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: 1.24 Time building geometry restraints manager: 0.93 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: 1382 1.31 - 1.44: 2451 1.44 - 1.57: 5144 1.57 - 1.70: 0 1.70 - 1.83: 94 Bond restraints: 9071 Sorted by residual: bond pdb=" C22 STI B 701 " pdb=" N21 STI B 701 " ideal model delta sigma weight residual 1.357 1.465 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C9 STI B 701 " pdb=" N13 STI B 701 " ideal model delta sigma weight residual 1.362 1.461 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C5 STI B 701 " pdb=" C7 STI B 701 " ideal model delta sigma weight residual 1.475 1.381 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C14 STI B 701 " pdb=" N13 STI B 701 " ideal model delta sigma weight residual 1.391 1.460 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C16 STI B 701 " pdb=" N21 STI B 701 " ideal model delta sigma weight residual 1.401 1.467 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 9066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 11669 2.08 - 4.16: 494 4.16 - 6.24: 85 6.24 - 8.32: 30 8.32 - 10.40: 8 Bond angle restraints: 12286 Sorted by residual: angle pdb=" C PHE A 266 " pdb=" N HIS A 267 " pdb=" CA HIS A 267 " ideal model delta sigma weight residual 122.36 132.15 -9.79 1.47e+00 4.63e-01 4.44e+01 angle pdb=" C PHE B 266 " pdb=" N HIS B 267 " pdb=" CA HIS B 267 " ideal model delta sigma weight residual 122.36 131.40 -9.04 1.47e+00 4.63e-01 3.78e+01 angle pdb=" C SER A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.33 124.81 -4.48 8.00e-01 1.56e+00 3.13e+01 angle pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " pdb=" CG GLU A 211 " ideal model delta sigma weight residual 114.10 124.50 -10.40 2.00e+00 2.50e-01 2.70e+01 angle pdb=" C ASN A 557 " pdb=" N LEU A 558 " pdb=" CA LEU A 558 " ideal model delta sigma weight residual 121.54 130.42 -8.88 1.91e+00 2.74e-01 2.16e+01 ... (remaining 12281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 4943 21.82 - 43.64: 456 43.64 - 65.46: 45 65.46 - 87.27: 10 87.27 - 109.09: 6 Dihedral angle restraints: 5460 sinusoidal: 2208 harmonic: 3252 Sorted by residual: dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual 93.00 25.59 67.41 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 25.84 67.16 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CA PHE A 266 " pdb=" C PHE A 266 " pdb=" N HIS A 267 " pdb=" CA HIS A 267 " ideal model delta harmonic sigma weight residual -180.00 -147.56 -32.44 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1164 0.069 - 0.137: 223 0.137 - 0.206: 27 0.206 - 0.274: 6 0.274 - 0.343: 4 Chirality restraints: 1424 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL B 173 " pdb=" CA VAL B 173 " pdb=" CG1 VAL B 173 " pdb=" CG2 VAL B 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE B 108 " pdb=" CA ILE B 108 " pdb=" CG1 ILE B 108 " pdb=" CG2 ILE B 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1421 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 484 " -0.047 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO A 485 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 484 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO B 485 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 257 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C THR A 257 " 0.044 2.00e-02 2.50e+03 pdb=" O THR A 257 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU A 258 " -0.015 2.00e-02 2.50e+03 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2170 2.78 - 3.31: 7827 3.31 - 3.84: 13788 3.84 - 4.37: 15420 4.37 - 4.90: 26342 Nonbonded interactions: 65547 Sorted by model distance: nonbonded pdb=" OH TYR A 413 " pdb=" O LEU B 555 " model vdw 2.245 3.040 nonbonded pdb=" O SER B 440 " pdb=" OG SER B 440 " model vdw 2.283 3.040 nonbonded pdb=" NH1 ARG A 575 " pdb=" OG1 THR A 579 " model vdw 2.298 3.120 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 261 " model vdw 2.312 3.040 nonbonded pdb=" O ILE B 335 " pdb=" OG SER B 339 " model vdw 2.313 3.040 ... (remaining 65542 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 654) selection = (chain 'B' and resid 35 through 654) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 9074 Z= 0.306 Angle : 1.074 13.272 12292 Z= 0.592 Chirality : 0.060 0.343 1424 Planarity : 0.006 0.070 1519 Dihedral : 16.225 109.093 3363 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.87 % Favored : 89.95 % Rotamer: Outliers : 0.31 % Allowed : 13.20 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.42 (0.16), residues: 1114 helix: -4.61 (0.09), residues: 526 sheet: -4.53 (0.73), residues: 24 loop : -3.94 (0.20), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 575 TYR 0.014 0.002 TYR A 342 PHE 0.026 0.002 PHE A 489 TRP 0.009 0.001 TRP B 564 HIS 0.008 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 9071) covalent geometry : angle 1.06667 (12286) SS BOND : bond 0.06639 ( 3) SS BOND : angle 5.84212 ( 6) hydrogen bonds : bond 0.35125 ( 266) hydrogen bonds : angle 9.97133 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 127 ASP cc_start: 0.8178 (m-30) cc_final: 0.7975 (m-30) REVERT: A 190 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7438 (mp0) REVERT: A 523 MET cc_start: 0.9087 (ttt) cc_final: 0.8831 (ttm) REVERT: A 567 TRP cc_start: 0.8948 (p-90) cc_final: 0.8363 (p-90) REVERT: A 643 ILE cc_start: 0.9335 (pt) cc_final: 0.8922 (mt) REVERT: B 242 ILE cc_start: 0.9181 (tp) cc_final: 0.8971 (tp) REVERT: B 252 LEU cc_start: 0.9174 (tp) cc_final: 0.8967 (tp) REVERT: B 253 PHE cc_start: 0.8610 (m-10) cc_final: 0.8406 (m-80) REVERT: B 296 ASP cc_start: 0.7141 (t0) cc_final: 0.6752 (t0) REVERT: B 413 TYR cc_start: 0.8504 (m-80) cc_final: 0.8202 (m-80) REVERT: B 492 ILE cc_start: 0.8965 (tp) cc_final: 0.8757 (mm) REVERT: B 541 MET cc_start: 0.8506 (tmm) cc_final: 0.8232 (tmm) REVERT: B 548 MET cc_start: 0.8164 (mtt) cc_final: 0.7762 (mtt) REVERT: B 573 ILE cc_start: 0.9390 (mt) cc_final: 0.9148 (mt) REVERT: B 643 ILE cc_start: 0.9502 (pt) cc_final: 0.9212 (tt) outliers start: 3 outliers final: 2 residues processed: 196 average time/residue: 0.0870 time to fit residues: 24.1230 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain B residue 63 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 76 ASN A 109 ASN A 120 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 629 ASN B 76 ASN B 109 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN B 398 GLN B 418 ASN B 601 ASN B 629 ASN B 630 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099474 restraints weight = 17756.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102597 restraints weight = 9327.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104690 restraints weight = 6162.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106042 restraints weight = 4713.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106780 restraints weight = 3974.560| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9074 Z= 0.267 Angle : 0.813 9.329 12292 Z= 0.419 Chirality : 0.048 0.195 1424 Planarity : 0.005 0.055 1519 Dihedral : 8.798 83.611 1353 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.95 % Favored : 88.96 % Rotamer: Outliers : 4.05 % Allowed : 19.44 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.20), residues: 1114 helix: -2.71 (0.19), residues: 498 sheet: -5.10 (0.45), residues: 36 loop : -3.51 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.017 0.002 TYR B 413 PHE 0.019 0.002 PHE A 455 TRP 0.018 0.002 TRP A 379 HIS 0.008 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 9071) covalent geometry : angle 0.81313 (12286) SS BOND : bond 0.00299 ( 3) SS BOND : angle 1.19744 ( 6) hydrogen bonds : bond 0.06110 ( 266) hydrogen bonds : angle 5.18846 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.326 Fit side-chains REVERT: A 106 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8794 (m) REVERT: A 107 LEU cc_start: 0.8859 (mm) cc_final: 0.8575 (tp) REVERT: A 190 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7601 (mp0) REVERT: A 458 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8512 (mm-30) REVERT: A 483 MET cc_start: 0.7783 (tmm) cc_final: 0.7537 (tmm) REVERT: A 523 MET cc_start: 0.9256 (ttt) cc_final: 0.8931 (ttm) REVERT: A 567 TRP cc_start: 0.9005 (p-90) cc_final: 0.8409 (p-90) REVERT: A 635 CYS cc_start: 0.8818 (m) cc_final: 0.8500 (t) REVERT: B 199 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7992 (tp30) REVERT: B 211 GLU cc_start: 0.8109 (tt0) cc_final: 0.7828 (tt0) REVERT: B 242 ILE cc_start: 0.9163 (tp) cc_final: 0.8954 (tp) REVERT: B 253 PHE cc_start: 0.8688 (m-10) cc_final: 0.8341 (m-80) REVERT: B 296 ASP cc_start: 0.7175 (t0) cc_final: 0.6902 (t0) REVERT: B 385 PHE cc_start: 0.8600 (t80) cc_final: 0.8378 (t80) REVERT: B 413 TYR cc_start: 0.8661 (m-80) cc_final: 0.8131 (m-80) REVERT: B 458 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 492 ILE cc_start: 0.9050 (tp) cc_final: 0.8752 (tp) REVERT: B 514 MET cc_start: 0.8921 (tmm) cc_final: 0.8479 (tmm) REVERT: B 541 MET cc_start: 0.8833 (tmm) cc_final: 0.8209 (tmm) outliers start: 39 outliers final: 22 residues processed: 175 average time/residue: 0.0637 time to fit residues: 17.4022 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 642 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 569 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS B 289 ASN B 557 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102880 restraints weight = 17347.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106285 restraints weight = 8899.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108587 restraints weight = 5783.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109870 restraints weight = 4382.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110949 restraints weight = 3709.167| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9074 Z= 0.125 Angle : 0.660 8.982 12292 Z= 0.331 Chirality : 0.043 0.181 1424 Planarity : 0.004 0.053 1519 Dihedral : 7.476 73.657 1353 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.53 % Allowed : 22.56 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.23), residues: 1114 helix: -1.64 (0.22), residues: 490 sheet: -4.63 (0.65), residues: 24 loop : -3.22 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.016 0.001 TYR A 276 PHE 0.013 0.001 PHE B 506 TRP 0.010 0.001 TRP A 379 HIS 0.013 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9071) covalent geometry : angle 0.65965 (12286) SS BOND : bond 0.00687 ( 3) SS BOND : angle 1.13542 ( 6) hydrogen bonds : bond 0.04511 ( 266) hydrogen bonds : angle 4.32712 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 106 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8791 (m) REVERT: A 107 LEU cc_start: 0.8848 (mm) cc_final: 0.8620 (tp) REVERT: A 190 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7539 (mp0) REVERT: A 483 MET cc_start: 0.7692 (tmm) cc_final: 0.7371 (tmm) REVERT: A 523 MET cc_start: 0.9140 (ttt) cc_final: 0.8492 (ttp) REVERT: A 567 TRP cc_start: 0.8890 (p-90) cc_final: 0.8369 (p-90) REVERT: B 131 MET cc_start: 0.8645 (mmm) cc_final: 0.8309 (mmm) REVERT: B 155 HIS cc_start: 0.8333 (t70) cc_final: 0.8058 (t70) REVERT: B 199 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8082 (mm-30) REVERT: B 242 ILE cc_start: 0.9070 (tp) cc_final: 0.8841 (tp) REVERT: B 253 PHE cc_start: 0.8546 (m-10) cc_final: 0.8248 (m-80) REVERT: B 283 HIS cc_start: 0.7954 (t70) cc_final: 0.7642 (t70) REVERT: B 296 ASP cc_start: 0.7011 (t0) cc_final: 0.6704 (t0) REVERT: B 413 TYR cc_start: 0.8575 (m-80) cc_final: 0.8063 (m-80) REVERT: B 458 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 481 MET cc_start: 0.8503 (tpp) cc_final: 0.7880 (ttt) REVERT: B 492 ILE cc_start: 0.8986 (tp) cc_final: 0.8702 (tp) REVERT: B 496 MET cc_start: 0.8699 (tpp) cc_final: 0.8482 (tpp) REVERT: B 514 MET cc_start: 0.8867 (tmm) cc_final: 0.8393 (tmm) REVERT: B 515 MET cc_start: 0.8988 (tpp) cc_final: 0.8398 (tpp) REVERT: B 541 MET cc_start: 0.8603 (tmm) cc_final: 0.8179 (tmm) REVERT: B 548 MET cc_start: 0.7900 (mtt) cc_final: 0.7369 (mtm) REVERT: B 568 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9006 (tt) outliers start: 34 outliers final: 21 residues processed: 162 average time/residue: 0.0558 time to fit residues: 14.4114 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 603 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 0.0030 chunk 84 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 243 HIS B 557 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100732 restraints weight = 17591.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104068 restraints weight = 9248.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106189 restraints weight = 6087.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107673 restraints weight = 4647.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108202 restraints weight = 3899.450| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9074 Z= 0.165 Angle : 0.664 8.743 12292 Z= 0.336 Chirality : 0.045 0.245 1424 Planarity : 0.004 0.044 1519 Dihedral : 7.318 80.656 1353 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 5.51 % Allowed : 22.14 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.24), residues: 1114 helix: -1.11 (0.23), residues: 498 sheet: -4.54 (0.67), residues: 24 loop : -3.04 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.020 0.001 TYR A 463 PHE 0.012 0.001 PHE A 506 TRP 0.010 0.001 TRP A 379 HIS 0.013 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9071) covalent geometry : angle 0.66353 (12286) SS BOND : bond 0.00257 ( 3) SS BOND : angle 1.25721 ( 6) hydrogen bonds : bond 0.04131 ( 266) hydrogen bonds : angle 4.22589 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8891 (mm) cc_final: 0.8649 (tp) REVERT: A 190 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7580 (mp0) REVERT: A 475 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9390 (tt) REVERT: A 483 MET cc_start: 0.7860 (tmm) cc_final: 0.7453 (tmm) REVERT: A 523 MET cc_start: 0.9142 (ttt) cc_final: 0.8484 (ttp) REVERT: A 541 MET cc_start: 0.8030 (tmm) cc_final: 0.7408 (tmm) REVERT: A 567 TRP cc_start: 0.8942 (p-90) cc_final: 0.8397 (p-90) REVERT: A 645 TYR cc_start: 0.8903 (t80) cc_final: 0.8508 (t80) REVERT: B 131 MET cc_start: 0.8632 (mmm) cc_final: 0.8267 (mmm) REVERT: B 199 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8151 (mm-30) REVERT: B 242 ILE cc_start: 0.9081 (tp) cc_final: 0.8853 (tp) REVERT: B 253 PHE cc_start: 0.8506 (m-10) cc_final: 0.8132 (m-80) REVERT: B 413 TYR cc_start: 0.8672 (m-80) cc_final: 0.8164 (m-80) REVERT: B 458 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 492 ILE cc_start: 0.9019 (tp) cc_final: 0.8748 (tp) REVERT: B 514 MET cc_start: 0.8879 (tmm) cc_final: 0.8426 (tmm) REVERT: B 523 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7740 (ttp) REVERT: B 540 LEU cc_start: 0.9309 (tp) cc_final: 0.9079 (tt) REVERT: B 541 MET cc_start: 0.8596 (tmm) cc_final: 0.7888 (tmm) REVERT: B 548 MET cc_start: 0.7941 (mtt) cc_final: 0.7502 (mtm) REVERT: B 568 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9009 (tt) outliers start: 53 outliers final: 35 residues processed: 169 average time/residue: 0.0590 time to fit residues: 15.9594 Evaluate side-chains 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 642 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.130473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099068 restraints weight = 17632.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102318 restraints weight = 9362.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104463 restraints weight = 6224.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105697 restraints weight = 4749.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106750 restraints weight = 4037.866| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9074 Z= 0.200 Angle : 0.687 9.044 12292 Z= 0.346 Chirality : 0.045 0.199 1424 Planarity : 0.004 0.040 1519 Dihedral : 7.276 85.196 1353 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 5.93 % Allowed : 23.28 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.24), residues: 1114 helix: -0.95 (0.23), residues: 508 sheet: -4.80 (0.47), residues: 36 loop : -2.88 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.018 0.002 TYR A 463 PHE 0.014 0.002 PHE A 489 TRP 0.010 0.001 TRP A 379 HIS 0.005 0.001 HIS B 630 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9071) covalent geometry : angle 0.68715 (12286) SS BOND : bond 0.00107 ( 3) SS BOND : angle 1.14151 ( 6) hydrogen bonds : bond 0.04200 ( 266) hydrogen bonds : angle 4.32408 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7821 (pp) REVERT: A 190 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7630 (mp0) REVERT: A 458 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8235 (mm-30) REVERT: A 475 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9371 (tt) REVERT: A 483 MET cc_start: 0.8008 (tmm) cc_final: 0.7529 (tmm) REVERT: A 523 MET cc_start: 0.9099 (ttt) cc_final: 0.8494 (ttp) REVERT: A 541 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7325 (tmm) REVERT: A 567 TRP cc_start: 0.8997 (p-90) cc_final: 0.8443 (p-90) REVERT: A 645 TYR cc_start: 0.8883 (t80) cc_final: 0.8537 (t80) REVERT: B 131 MET cc_start: 0.8609 (mmm) cc_final: 0.8041 (mmm) REVERT: B 199 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8139 (mm-30) REVERT: B 242 ILE cc_start: 0.9059 (tp) cc_final: 0.8820 (tp) REVERT: B 253 PHE cc_start: 0.8501 (m-10) cc_final: 0.8095 (m-80) REVERT: B 413 TYR cc_start: 0.8560 (m-80) cc_final: 0.8073 (m-80) REVERT: B 458 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7464 (mt-10) REVERT: B 475 LEU cc_start: 0.9346 (tt) cc_final: 0.9126 (tp) REVERT: B 481 MET cc_start: 0.8314 (tpp) cc_final: 0.7759 (ttm) REVERT: B 492 ILE cc_start: 0.9032 (tp) cc_final: 0.8750 (tp) REVERT: B 496 MET cc_start: 0.8703 (tpp) cc_final: 0.8467 (tpp) REVERT: B 523 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.7744 (ttp) REVERT: B 540 LEU cc_start: 0.9408 (tp) cc_final: 0.9114 (tt) REVERT: B 541 MET cc_start: 0.8655 (tmm) cc_final: 0.7953 (tmm) REVERT: B 548 MET cc_start: 0.8072 (mtt) cc_final: 0.7574 (mtm) REVERT: B 568 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9047 (tt) REVERT: B 573 ILE cc_start: 0.9223 (mt) cc_final: 0.8727 (mt) outliers start: 57 outliers final: 40 residues processed: 168 average time/residue: 0.0569 time to fit residues: 15.5054 Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS B 557 ASN B 583 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102560 restraints weight = 17377.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105805 restraints weight = 9162.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108023 restraints weight = 6110.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109466 restraints weight = 4645.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110279 restraints weight = 3907.702| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9074 Z= 0.116 Angle : 0.631 10.903 12292 Z= 0.310 Chirality : 0.043 0.312 1424 Planarity : 0.004 0.039 1519 Dihedral : 6.943 75.077 1353 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.37 % Allowed : 26.61 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.25), residues: 1114 helix: -0.40 (0.25), residues: 492 sheet: -4.45 (0.67), residues: 24 loop : -2.85 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.031 0.001 TYR B 336 PHE 0.013 0.001 PHE A 506 TRP 0.008 0.001 TRP A 379 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9071) covalent geometry : angle 0.63093 (12286) SS BOND : bond 0.00082 ( 3) SS BOND : angle 0.75817 ( 6) hydrogen bonds : bond 0.03600 ( 266) hydrogen bonds : angle 3.91650 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9429 (pt) cc_final: 0.8926 (mm) REVERT: A 190 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7615 (mp0) REVERT: A 458 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 475 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9365 (tt) REVERT: A 483 MET cc_start: 0.7925 (tmm) cc_final: 0.7427 (tmm) REVERT: A 523 MET cc_start: 0.9035 (ttt) cc_final: 0.8354 (ttp) REVERT: A 541 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7656 (tmm) REVERT: A 567 TRP cc_start: 0.8883 (p-90) cc_final: 0.8346 (p-90) REVERT: A 645 TYR cc_start: 0.8867 (t80) cc_final: 0.8631 (t80) REVERT: B 131 MET cc_start: 0.8571 (mmm) cc_final: 0.7846 (mmm) REVERT: B 199 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 242 ILE cc_start: 0.9002 (tp) cc_final: 0.8769 (tp) REVERT: B 253 PHE cc_start: 0.8388 (m-10) cc_final: 0.8024 (m-80) REVERT: B 413 TYR cc_start: 0.8616 (m-80) cc_final: 0.8115 (m-80) REVERT: B 475 LEU cc_start: 0.9288 (tt) cc_final: 0.9067 (tp) REVERT: B 481 MET cc_start: 0.8441 (tpp) cc_final: 0.7912 (ttt) REVERT: B 492 ILE cc_start: 0.8993 (tp) cc_final: 0.8706 (tp) REVERT: B 514 MET cc_start: 0.8942 (tmm) cc_final: 0.8350 (tmm) REVERT: B 523 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7663 (ttp) REVERT: B 541 MET cc_start: 0.8618 (tmm) cc_final: 0.8065 (tmm) REVERT: B 548 MET cc_start: 0.7957 (mtt) cc_final: 0.7314 (mtm) REVERT: B 568 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8967 (tt) REVERT: B 573 ILE cc_start: 0.9230 (mt) cc_final: 0.8604 (mp) REVERT: B 636 MET cc_start: 0.9118 (tpp) cc_final: 0.8890 (tpp) outliers start: 42 outliers final: 30 residues processed: 165 average time/residue: 0.0578 time to fit residues: 15.1372 Evaluate side-chains 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100803 restraints weight = 17583.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104032 restraints weight = 9330.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106135 restraints weight = 6194.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107506 restraints weight = 4772.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108095 restraints weight = 4040.529| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9074 Z= 0.174 Angle : 0.670 9.774 12292 Z= 0.334 Chirality : 0.045 0.264 1424 Planarity : 0.004 0.052 1519 Dihedral : 7.005 82.514 1353 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.09 % Allowed : 26.92 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.25), residues: 1114 helix: -0.42 (0.24), residues: 506 sheet: -4.56 (0.64), residues: 24 loop : -2.77 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.039 0.002 TYR B 336 PHE 0.020 0.001 PHE B 506 TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 630 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9071) covalent geometry : angle 0.66955 (12286) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.91387 ( 6) hydrogen bonds : bond 0.03837 ( 266) hydrogen bonds : angle 4.10314 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7640 (pp) REVERT: A 190 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7655 (mp0) REVERT: A 199 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8014 (tp30) REVERT: A 458 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8375 (tp30) REVERT: A 475 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9368 (tt) REVERT: A 483 MET cc_start: 0.7990 (tmm) cc_final: 0.7498 (tmm) REVERT: A 523 MET cc_start: 0.9087 (ttt) cc_final: 0.8441 (ttp) REVERT: A 541 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7285 (tmm) REVERT: A 567 TRP cc_start: 0.8931 (p-90) cc_final: 0.8356 (p-90) REVERT: B 131 MET cc_start: 0.8539 (mmm) cc_final: 0.7865 (mmm) REVERT: B 155 HIS cc_start: 0.8477 (t70) cc_final: 0.8214 (t70) REVERT: B 242 ILE cc_start: 0.9027 (tp) cc_final: 0.8795 (tp) REVERT: B 253 PHE cc_start: 0.8416 (m-10) cc_final: 0.7981 (m-80) REVERT: B 413 TYR cc_start: 0.8603 (m-80) cc_final: 0.8113 (m-80) REVERT: B 458 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8395 (mm-30) REVERT: B 492 ILE cc_start: 0.8964 (tp) cc_final: 0.8719 (tp) REVERT: B 496 MET cc_start: 0.8703 (tpp) cc_final: 0.8471 (tpp) REVERT: B 514 MET cc_start: 0.8845 (tmm) cc_final: 0.8561 (tmm) REVERT: B 523 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7760 (ttp) REVERT: B 541 MET cc_start: 0.8587 (tmm) cc_final: 0.8131 (tmm) REVERT: B 548 MET cc_start: 0.8036 (mtt) cc_final: 0.7448 (mtm) REVERT: B 568 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9012 (tt) REVERT: B 573 ILE cc_start: 0.9216 (mt) cc_final: 0.8584 (mp) outliers start: 49 outliers final: 37 residues processed: 170 average time/residue: 0.0556 time to fit residues: 15.2560 Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099684 restraints weight = 17540.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102738 restraints weight = 9435.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104845 restraints weight = 6375.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105904 restraints weight = 4894.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107063 restraints weight = 4186.457| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9074 Z= 0.203 Angle : 0.708 9.818 12292 Z= 0.353 Chirality : 0.046 0.228 1424 Planarity : 0.004 0.043 1519 Dihedral : 7.099 86.314 1353 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 5.30 % Allowed : 26.61 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.25), residues: 1114 helix: -0.39 (0.24), residues: 508 sheet: -4.81 (0.46), residues: 36 loop : -2.74 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.038 0.002 TYR B 336 PHE 0.026 0.002 PHE B 506 TRP 0.008 0.001 TRP A 379 HIS 0.005 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9071) covalent geometry : angle 0.70780 (12286) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.97508 ( 6) hydrogen bonds : bond 0.04118 ( 266) hydrogen bonds : angle 4.20133 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9439 (pt) cc_final: 0.9091 (mm) REVERT: A 127 ASP cc_start: 0.8656 (t0) cc_final: 0.8388 (t0) REVERT: A 148 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7655 (pp) REVERT: A 190 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7658 (mp0) REVERT: A 199 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7913 (tp30) REVERT: A 458 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8429 (tp30) REVERT: A 475 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9345 (tt) REVERT: A 483 MET cc_start: 0.8088 (tmm) cc_final: 0.7556 (tmm) REVERT: A 523 MET cc_start: 0.9037 (ttt) cc_final: 0.8828 (tmm) REVERT: A 541 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7541 (tmm) REVERT: A 567 TRP cc_start: 0.8953 (p-90) cc_final: 0.8376 (p-90) REVERT: B 242 ILE cc_start: 0.9009 (tp) cc_final: 0.8773 (tp) REVERT: B 253 PHE cc_start: 0.8423 (m-10) cc_final: 0.7959 (m-80) REVERT: B 413 TYR cc_start: 0.8572 (m-80) cc_final: 0.8084 (m-80) REVERT: B 458 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8466 (mm-30) REVERT: B 481 MET cc_start: 0.8480 (tpp) cc_final: 0.7951 (ttm) REVERT: B 492 ILE cc_start: 0.8927 (tp) cc_final: 0.8679 (tp) REVERT: B 523 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7711 (ttp) REVERT: B 541 MET cc_start: 0.8558 (tmm) cc_final: 0.8143 (tmm) REVERT: B 548 MET cc_start: 0.8070 (mtt) cc_final: 0.7541 (mtm) REVERT: B 568 LEU cc_start: 0.9327 (tp) cc_final: 0.9066 (tt) REVERT: B 573 ILE cc_start: 0.9234 (mt) cc_final: 0.8653 (mp) outliers start: 51 outliers final: 44 residues processed: 165 average time/residue: 0.0632 time to fit residues: 16.4460 Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.0870 chunk 3 optimal weight: 0.0040 chunk 109 optimal weight: 0.0670 chunk 17 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 0.3908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 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 = 0.3799 r_free = 0.3799 target = 0.136826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106003 restraints weight = 17201.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109357 restraints weight = 8982.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111643 restraints weight = 5892.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113145 restraints weight = 4459.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113582 restraints weight = 3726.268| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9074 Z= 0.111 Angle : 0.644 10.904 12292 Z= 0.316 Chirality : 0.043 0.222 1424 Planarity : 0.004 0.043 1519 Dihedral : 6.652 70.494 1353 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.01 % Allowed : 28.79 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.26), residues: 1114 helix: 0.08 (0.25), residues: 492 sheet: -4.29 (0.71), residues: 24 loop : -2.68 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.030 0.001 TYR A 645 PHE 0.018 0.001 PHE B 506 TRP 0.010 0.001 TRP A 379 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9071) covalent geometry : angle 0.64449 (12286) SS BOND : bond 0.00056 ( 3) SS BOND : angle 0.60273 ( 6) hydrogen bonds : bond 0.03293 ( 266) hydrogen bonds : angle 3.65348 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9472 (pt) cc_final: 0.9154 (mm) REVERT: A 148 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7908 (pp) REVERT: A 190 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7506 (mp0) REVERT: A 483 MET cc_start: 0.7898 (tmm) cc_final: 0.7413 (tmm) REVERT: A 541 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7406 (tmm) REVERT: B 131 MET cc_start: 0.8568 (mmm) cc_final: 0.7765 (mmm) REVERT: B 253 PHE cc_start: 0.8305 (m-10) cc_final: 0.7945 (m-80) REVERT: B 413 TYR cc_start: 0.8434 (m-80) cc_final: 0.8053 (m-80) REVERT: B 458 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8323 (mm-30) REVERT: B 481 MET cc_start: 0.8407 (tpp) cc_final: 0.7848 (ttm) REVERT: B 492 ILE cc_start: 0.8845 (tp) cc_final: 0.8615 (tp) REVERT: B 514 MET cc_start: 0.9023 (tmm) cc_final: 0.8556 (tmm) REVERT: B 523 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.7608 (ttp) REVERT: B 541 MET cc_start: 0.8387 (tmm) cc_final: 0.7890 (tmm) REVERT: B 548 MET cc_start: 0.8035 (mtt) cc_final: 0.7454 (mtm) REVERT: B 568 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8951 (tt) REVERT: B 573 ILE cc_start: 0.9274 (mt) cc_final: 0.8674 (mp) REVERT: B 636 MET cc_start: 0.9054 (tpp) cc_final: 0.8759 (tpp) outliers start: 29 outliers final: 19 residues processed: 155 average time/residue: 0.0622 time to fit residues: 15.4039 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 12 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 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 = 0.3782 r_free = 0.3782 target = 0.135597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104881 restraints weight = 17239.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108179 restraints weight = 9069.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110335 restraints weight = 5999.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111852 restraints weight = 4586.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112764 restraints weight = 3828.977| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9074 Z= 0.123 Angle : 0.667 11.250 12292 Z= 0.326 Chirality : 0.044 0.247 1424 Planarity : 0.004 0.041 1519 Dihedral : 6.613 74.307 1351 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.70 % Allowed : 29.52 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.26), residues: 1114 helix: 0.08 (0.25), residues: 504 sheet: -4.25 (0.73), residues: 24 loop : -2.71 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.029 0.002 TYR A 494 PHE 0.021 0.001 PHE A 506 TRP 0.008 0.001 TRP A 379 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9071) covalent geometry : angle 0.66674 (12286) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.66393 ( 6) hydrogen bonds : bond 0.03348 ( 266) hydrogen bonds : angle 3.65913 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9487 (pt) cc_final: 0.9223 (mm) REVERT: A 148 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7902 (pp) REVERT: A 190 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7516 (mp0) REVERT: A 483 MET cc_start: 0.7953 (tmm) cc_final: 0.7415 (tmm) REVERT: A 523 MET cc_start: 0.9167 (ttp) cc_final: 0.8874 (tmm) REVERT: A 541 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7237 (tmm) REVERT: B 131 MET cc_start: 0.8567 (mmm) cc_final: 0.8330 (mmm) REVERT: B 253 PHE cc_start: 0.8344 (m-10) cc_final: 0.7948 (m-80) REVERT: B 413 TYR cc_start: 0.8529 (m-80) cc_final: 0.8149 (m-80) REVERT: B 458 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8376 (mm-30) REVERT: B 475 LEU cc_start: 0.9189 (tt) cc_final: 0.8719 (tp) REVERT: B 481 MET cc_start: 0.8571 (tpp) cc_final: 0.8023 (ttt) REVERT: B 492 ILE cc_start: 0.8824 (tp) cc_final: 0.8591 (tp) REVERT: B 496 MET cc_start: 0.8734 (tpp) cc_final: 0.8509 (tpp) REVERT: B 523 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7707 (ttp) REVERT: B 541 MET cc_start: 0.8543 (tmm) cc_final: 0.7953 (tmm) REVERT: B 548 MET cc_start: 0.8027 (mtt) cc_final: 0.7461 (mtm) REVERT: B 568 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8977 (tt) REVERT: B 573 ILE cc_start: 0.9279 (mt) cc_final: 0.8659 (mp) REVERT: B 636 MET cc_start: 0.9069 (tpp) cc_final: 0.8812 (tpp) outliers start: 26 outliers final: 21 residues processed: 145 average time/residue: 0.0671 time to fit residues: 15.3988 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 59 optimal weight: 0.0030 chunk 58 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 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 = 0.3812 r_free = 0.3812 target = 0.137935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107267 restraints weight = 17031.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110595 restraints weight = 8993.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112841 restraints weight = 5908.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114305 restraints weight = 4483.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115087 restraints weight = 3748.259| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9074 Z= 0.110 Angle : 0.656 11.167 12292 Z= 0.318 Chirality : 0.043 0.244 1424 Planarity : 0.003 0.042 1519 Dihedral : 6.451 71.039 1351 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.60 % Allowed : 29.94 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.26), residues: 1114 helix: 0.18 (0.25), residues: 508 sheet: -4.05 (0.80), residues: 24 loop : -2.64 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 236 TYR 0.031 0.002 TYR A 645 PHE 0.021 0.001 PHE A 506 TRP 0.009 0.001 TRP A 379 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9071) covalent geometry : angle 0.65563 (12286) SS BOND : bond 0.00046 ( 3) SS BOND : angle 0.61867 ( 6) hydrogen bonds : bond 0.03123 ( 266) hydrogen bonds : angle 3.51480 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1279.00 seconds wall clock time: 22 minutes 54.32 seconds (1374.32 seconds total)