Starting phenix.real_space_refine on Thu Feb 13 17:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxh_21437/02_2025/6vxh_21437.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxh_21437/02_2025/6vxh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxh_21437/02_2025/6vxh_21437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxh_21437/02_2025/6vxh_21437.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxh_21437/02_2025/6vxh_21437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxh_21437/02_2025/6vxh_21437.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.44, per 1000 atoms: 0.61 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.84 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: 2.13 Time building geometry restraints manager: 2.59 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: 0.610 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.120 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- 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 0.108 9071 Z= 0.413 Angle : 1.067 10.399 12286 Z= 0.589 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 : 5.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B 564 HIS 0.008 0.001 HIS A 267 PHE 0.026 0.002 PHE A 489 TYR 0.014 0.002 TYR A 342 ARG 0.006 0.001 ARG A 575 *********************** 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 : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8114 (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: 0.8830 (ttm) REVERT: A 567 TRP cc_start: 0.8948 (p-90) cc_final: 0.8364 (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: 0.8970 (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: 0.8407 (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: 0.8197 (m-80) REVERT: B 492 ILE cc_start: 0.8965 (tp) cc_final: 0.8753 (mm) REVERT: B 541 MET cc_start: 0.8505 (tmm) cc_final: 0.8235 (tmm) REVERT: B 548 MET cc_start: 0.8164 (mtt) cc_final: 0.7777 (mtt) REVERT: B 549 MET cc_start: 0.8392 (ttp) cc_final: 0.8182 (tmm) 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: 0.9211 (tt) outliers start: 3 outliers final: 2 residues processed: 196 average time/residue: 0.2057 time to fit residues: 56.2344 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 : 0.965 ------------------------------------------------------------------------------- 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 94 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.0170 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101284 restraints weight = 17258.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104643 restraints weight = 8944.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106897 restraints weight = 5832.750| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9071 Z= 0.253 Angle : 0.743 9.738 12286 Z= 0.379 Chirality : 0.045 0.174 1424 Planarity : 0.005 0.056 1519 Dihedral : 8.646 74.201 1353 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.25 % Favored : 90.66 % Rotamer: Outliers : 3.22 % Allowed : 19.02 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.20), residues: 1114 helix: -2.64 (0.19), residues: 492 sheet: -4.56 (0.67), residues: 24 loop : -3.50 (0.21), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 379 HIS 0.008 0.001 HIS A 243 PHE 0.014 0.002 PHE A 455 TYR 0.013 0.001 TYR B 342 ARG 0.004 0.000 ARG B 426 *********************** 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 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.983 Fit side-chains REVERT: A 71 MET cc_start: 0.8443 (mmt) cc_final: 0.8191 (mmt) REVERT: A 107 LEU cc_start: 0.8865 (mm) cc_final: 0.8613 (tp) REVERT: A 124 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8758 (m) REVERT: A 190 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7585 (mp0) REVERT: A 283 HIS cc_start: 0.5958 (m-70) cc_final: 0.5591 (m-70) REVERT: A 458 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8536 (mm-30) REVERT: A 483 MET cc_start: 0.7575 (tmm) cc_final: 0.7349 (tmm) REVERT: A 522 SER cc_start: 0.9244 (t) cc_final: 0.9022 (t) REVERT: A 523 MET cc_start: 0.9220 (ttt) cc_final: 0.8888 (ttp) REVERT: A 567 TRP cc_start: 0.8944 (p-90) cc_final: 0.8376 (p-90) REVERT: A 635 CYS cc_start: 0.8835 (m) cc_final: 0.8556 (t) REVERT: B 131 MET cc_start: 0.8681 (mmm) cc_final: 0.8241 (mmm) REVERT: B 199 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7798 (tp30) REVERT: B 252 LEU cc_start: 0.9210 (tp) cc_final: 0.8965 (tp) REVERT: B 253 PHE cc_start: 0.8651 (m-10) cc_final: 0.8397 (m-80) REVERT: B 296 ASP cc_start: 0.7187 (t0) cc_final: 0.6903 (t0) REVERT: B 385 PHE cc_start: 0.8519 (t80) cc_final: 0.8310 (t80) REVERT: B 413 TYR cc_start: 0.8600 (m-80) cc_final: 0.8129 (m-80) REVERT: B 458 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 481 MET cc_start: 0.8641 (tpp) cc_final: 0.8038 (ttt) REVERT: B 492 ILE cc_start: 0.9014 (tp) cc_final: 0.8709 (tp) REVERT: B 514 MET cc_start: 0.8826 (tmm) cc_final: 0.8341 (tmm) REVERT: B 541 MET cc_start: 0.8729 (tmm) cc_final: 0.8037 (tmm) outliers start: 31 outliers final: 17 residues processed: 170 average time/residue: 0.1528 time to fit residues: 39.7291 Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE 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 206 ILE 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 63 ILE Chi-restraints excluded: chain B residue 68 ASN 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 642 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN B 40 HIS B 243 HIS ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS B 583 HIS B 629 ASN B 630 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095963 restraints weight = 17840.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099135 restraints weight = 9508.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101234 restraints weight = 6296.708| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9071 Z= 0.449 Angle : 0.831 9.176 12286 Z= 0.423 Chirality : 0.050 0.213 1424 Planarity : 0.005 0.049 1519 Dihedral : 7.881 88.676 1353 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 5.82 % Allowed : 21.52 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.22), residues: 1114 helix: -1.91 (0.21), residues: 500 sheet: -5.05 (0.44), residues: 36 loop : -3.25 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 379 HIS 0.013 0.002 HIS B 243 PHE 0.020 0.002 PHE A 489 TYR 0.020 0.002 TYR B 413 ARG 0.005 0.001 ARG A 163 *********************** 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 182 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8845 (mm) cc_final: 0.8606 (tp) REVERT: A 190 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7659 (mp0) REVERT: A 458 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8561 (mm-30) REVERT: A 475 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9412 (tt) REVERT: A 483 MET cc_start: 0.7969 (tmm) cc_final: 0.7610 (tmm) REVERT: A 523 MET cc_start: 0.9205 (ttt) cc_final: 0.8611 (ttp) REVERT: A 541 MET cc_start: 0.8141 (tmm) cc_final: 0.7807 (tmm) REVERT: A 567 TRP cc_start: 0.9045 (p-90) cc_final: 0.8458 (p-90) REVERT: B 90 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8287 (tt) REVERT: B 155 HIS cc_start: 0.8404 (t70) cc_final: 0.8050 (t70) REVERT: B 199 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 211 GLU cc_start: 0.8075 (tt0) cc_final: 0.7844 (tt0) REVERT: B 253 PHE cc_start: 0.8683 (m-10) cc_final: 0.8255 (m-80) REVERT: B 296 ASP cc_start: 0.7019 (t0) cc_final: 0.6699 (t0) REVERT: B 413 TYR cc_start: 0.8666 (m-80) cc_final: 0.8204 (m-80) REVERT: B 458 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7584 (mt-10) REVERT: B 492 ILE cc_start: 0.9075 (tp) cc_final: 0.8785 (tp) REVERT: B 496 MET cc_start: 0.8665 (tpp) cc_final: 0.8424 (tpp) REVERT: B 509 MET cc_start: 0.9137 (ttt) cc_final: 0.8850 (ttt) REVERT: B 541 MET cc_start: 0.8574 (tmm) cc_final: 0.8115 (tmm) REVERT: B 568 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9100 (tt) outliers start: 56 outliers final: 37 residues processed: 167 average time/residue: 0.1440 time to fit residues: 37.7320 Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 295 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 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 631 VAL 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 90 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 295 LEU 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 435 THR Chi-restraints excluded: chain B residue 487 ILE 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 639 ILE Chi-restraints excluded: chain B residue 642 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN B 289 ASN B 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103086 restraints weight = 17185.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106481 restraints weight = 8995.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108500 restraints weight = 5897.546| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9071 Z= 0.168 Angle : 0.649 10.042 12286 Z= 0.323 Chirality : 0.044 0.435 1424 Planarity : 0.004 0.039 1519 Dihedral : 7.223 72.054 1353 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.85 % Allowed : 24.74 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.24), residues: 1114 helix: -1.12 (0.23), residues: 494 sheet: -4.57 (0.66), residues: 24 loop : -3.08 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.005 0.001 HIS B 267 PHE 0.013 0.001 PHE A 506 TYR 0.010 0.001 TYR B 342 ARG 0.003 0.000 ARG A 163 *********************** 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 183 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8641 (m) REVERT: A 190 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7558 (mp0) REVERT: A 483 MET cc_start: 0.7719 (tmm) cc_final: 0.7299 (tmm) REVERT: A 523 MET cc_start: 0.9086 (ttt) cc_final: 0.8421 (ttp) REVERT: A 567 TRP cc_start: 0.8872 (p-90) cc_final: 0.8343 (p-90) REVERT: A 645 TYR cc_start: 0.8877 (t80) cc_final: 0.8386 (t80) REVERT: B 70 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 155 HIS cc_start: 0.8456 (t70) cc_final: 0.8118 (t70) REVERT: B 199 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8112 (mm-30) REVERT: B 253 PHE cc_start: 0.8519 (m-10) cc_final: 0.8208 (m-80) REVERT: B 413 TYR cc_start: 0.8627 (m-80) cc_final: 0.8114 (m-80) REVERT: B 458 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 481 MET cc_start: 0.8511 (tpp) cc_final: 0.7903 (ttt) REVERT: B 492 ILE cc_start: 0.9004 (tp) cc_final: 0.8713 (tp) REVERT: B 496 MET cc_start: 0.8793 (tpp) cc_final: 0.8556 (tpp) REVERT: B 514 MET cc_start: 0.9002 (tmm) cc_final: 0.8604 (tmm) REVERT: B 515 MET cc_start: 0.8848 (tpp) cc_final: 0.8302 (tpp) REVERT: B 523 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: B 541 MET cc_start: 0.8574 (tmm) cc_final: 0.7817 (tmm) REVERT: B 568 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9013 (tt) REVERT: B 573 ILE cc_start: 0.9260 (mt) cc_final: 0.8982 (mt) outliers start: 37 outliers final: 19 residues processed: 169 average time/residue: 0.1511 time to fit residues: 39.2483 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 450 VAL 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 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 206 ILE 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 603 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 83 optimal weight: 0.0070 chunk 86 optimal weight: 0.0050 chunk 100 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 2.2016 ------------------------------------------------------------------------------- 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 283 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101057 restraints weight = 17366.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104362 restraints weight = 9156.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106463 restraints weight = 6040.028| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9071 Z= 0.239 Angle : 0.661 9.163 12286 Z= 0.330 Chirality : 0.044 0.304 1424 Planarity : 0.004 0.037 1519 Dihedral : 7.143 79.626 1353 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.41 % Allowed : 25.26 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.24), residues: 1114 helix: -0.87 (0.23), residues: 504 sheet: -4.54 (0.66), residues: 24 loop : -2.94 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.005 0.001 HIS B 267 PHE 0.021 0.001 PHE A 506 TYR 0.024 0.002 TYR A 494 ARG 0.003 0.000 ARG A 96 *********************** 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 185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8682 (m) REVERT: A 148 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7769 (pp) REVERT: A 190 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7570 (mp0) REVERT: A 424 GLN cc_start: 0.9073 (pt0) cc_final: 0.8839 (pt0) REVERT: A 458 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 475 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9399 (tt) REVERT: A 483 MET cc_start: 0.7939 (tmm) cc_final: 0.7454 (tmm) REVERT: A 496 MET cc_start: 0.8413 (ttp) cc_final: 0.8105 (ttm) REVERT: A 523 MET cc_start: 0.9101 (ttt) cc_final: 0.8441 (ttp) REVERT: A 541 MET cc_start: 0.7971 (tmm) cc_final: 0.7546 (tmm) REVERT: A 567 TRP cc_start: 0.8937 (p-90) cc_final: 0.8379 (p-90) REVERT: A 645 TYR cc_start: 0.8869 (t80) cc_final: 0.8626 (t80) REVERT: B 131 MET cc_start: 0.8492 (mmm) cc_final: 0.8009 (mmm) REVERT: B 155 HIS cc_start: 0.8551 (t70) cc_final: 0.8176 (t70) REVERT: B 199 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 253 PHE cc_start: 0.8492 (m-10) cc_final: 0.8095 (m-80) REVERT: B 413 TYR cc_start: 0.8598 (m-80) cc_final: 0.8096 (m-80) REVERT: B 458 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7494 (mt-10) REVERT: B 492 ILE cc_start: 0.9022 (tp) cc_final: 0.8747 (tp) REVERT: B 514 MET cc_start: 0.9067 (tmm) cc_final: 0.8625 (tmm) REVERT: B 523 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.7731 (ttp) REVERT: B 540 LEU cc_start: 0.9156 (tt) cc_final: 0.8946 (tp) REVERT: B 541 MET cc_start: 0.8599 (tmm) cc_final: 0.7920 (tmm) REVERT: B 568 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9044 (tt) outliers start: 52 outliers final: 31 residues processed: 170 average time/residue: 0.1450 time to fit residues: 38.0980 Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 124 VAL 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 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 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 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 401 VAL Chi-restraints excluded: chain B residue 403 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 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 89 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.0370 chunk 24 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 4.5664 ------------------------------------------------------------------------------- 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 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096821 restraints weight = 17563.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099951 restraints weight = 9412.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101960 restraints weight = 6279.546| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9071 Z= 0.406 Angle : 0.778 9.500 12286 Z= 0.390 Chirality : 0.049 0.338 1424 Planarity : 0.004 0.039 1519 Dihedral : 7.401 88.740 1353 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 6.34 % Allowed : 25.36 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.24), residues: 1114 helix: -0.85 (0.23), residues: 498 sheet: -4.86 (0.46), residues: 36 loop : -2.93 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.006 0.001 HIS B 630 PHE 0.019 0.002 PHE A 506 TYR 0.023 0.002 TYR A 463 ARG 0.004 0.000 ARG A 96 *********************** 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 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8826 (t0) cc_final: 0.8578 (t0) REVERT: A 148 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7985 (pp) REVERT: A 190 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7502 (mp0) REVERT: A 458 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8471 (mm-30) REVERT: A 475 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9395 (tt) REVERT: A 483 MET cc_start: 0.8158 (tmm) cc_final: 0.7679 (tmm) REVERT: A 523 MET cc_start: 0.9113 (ttt) cc_final: 0.8524 (ttp) REVERT: A 567 TRP cc_start: 0.9029 (p-90) cc_final: 0.8437 (p-90) REVERT: B 155 HIS cc_start: 0.8666 (t70) cc_final: 0.8113 (t70) REVERT: B 199 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 253 PHE cc_start: 0.8458 (m-10) cc_final: 0.7936 (m-80) REVERT: B 336 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: B 413 TYR cc_start: 0.8652 (m-80) cc_final: 0.8182 (m-80) REVERT: B 458 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 492 ILE cc_start: 0.9034 (tp) cc_final: 0.8756 (tp) REVERT: B 496 MET cc_start: 0.8697 (tpp) cc_final: 0.8482 (tpp) REVERT: B 523 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7800 (ttp) REVERT: B 541 MET cc_start: 0.8656 (tmm) cc_final: 0.8027 (tmm) REVERT: B 568 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9098 (tt) REVERT: B 636 MET cc_start: 0.9214 (tpp) cc_final: 0.8772 (mmm) outliers start: 61 outliers final: 42 residues processed: 171 average time/residue: 0.1435 time to fit residues: 38.1344 Evaluate side-chains 169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain A residue 203 ASP 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 332 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 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 642 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL 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 108 ILE Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 377 LEU 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 435 THR 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 603 CYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS B 424 GLN B 557 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102683 restraints weight = 17168.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106017 restraints weight = 9001.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108221 restraints weight = 5911.454| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9071 Z= 0.179 Angle : 0.674 10.846 12286 Z= 0.328 Chirality : 0.044 0.369 1424 Planarity : 0.004 0.058 1519 Dihedral : 6.908 74.910 1353 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 4.05 % Allowed : 28.69 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.25), residues: 1114 helix: -0.48 (0.24), residues: 504 sheet: -4.61 (0.62), residues: 24 loop : -2.82 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.005 0.001 HIS B 267 PHE 0.017 0.001 PHE A 506 TYR 0.029 0.002 TYR A 645 ARG 0.003 0.000 ARG A 96 *********************** 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 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8717 (t0) cc_final: 0.8451 (t0) REVERT: A 458 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8239 (mm-30) REVERT: A 483 MET cc_start: 0.7946 (tmm) cc_final: 0.7374 (tmm) REVERT: A 523 MET cc_start: 0.9024 (ttt) cc_final: 0.8329 (ttp) REVERT: A 567 TRP cc_start: 0.8947 (p-90) cc_final: 0.8395 (p-90) REVERT: B 131 MET cc_start: 0.8536 (mmm) cc_final: 0.7325 (mmm) REVERT: B 155 HIS cc_start: 0.8706 (t70) cc_final: 0.8289 (t70) REVERT: B 199 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8110 (mm-30) REVERT: B 253 PHE cc_start: 0.8377 (m-10) cc_final: 0.7975 (m-80) REVERT: B 336 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: B 413 TYR cc_start: 0.8661 (m-80) cc_final: 0.8095 (m-80) REVERT: B 458 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7451 (mt-10) REVERT: B 481 MET cc_start: 0.8400 (tpp) cc_final: 0.7944 (ttt) REVERT: B 492 ILE cc_start: 0.8977 (tp) cc_final: 0.8695 (tp) REVERT: B 496 MET cc_start: 0.8778 (tpp) cc_final: 0.8534 (tpp) REVERT: B 514 MET cc_start: 0.9142 (tmm) cc_final: 0.8811 (tmm) REVERT: B 523 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: B 541 MET cc_start: 0.8443 (tmm) cc_final: 0.7951 (tmm) REVERT: B 568 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9007 (tt) outliers start: 39 outliers final: 25 residues processed: 166 average time/residue: 0.1441 time to fit residues: 37.1432 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 109 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 ASP 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 492 ILE 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 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU 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 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 28 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 62 optimal weight: 0.0370 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102886 restraints weight = 17423.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106202 restraints weight = 9082.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108472 restraints weight = 5939.428| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9071 Z= 0.193 Angle : 0.675 11.607 12286 Z= 0.328 Chirality : 0.044 0.376 1424 Planarity : 0.004 0.044 1519 Dihedral : 6.794 76.620 1353 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 3.43 % Allowed : 29.52 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.25), residues: 1114 helix: -0.19 (0.25), residues: 492 sheet: -4.47 (0.66), residues: 24 loop : -2.76 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS B 267 PHE 0.016 0.001 PHE A 506 TYR 0.026 0.002 TYR A 645 ARG 0.003 0.000 ARG A 96 *********************** 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 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9463 (pt) cc_final: 0.9118 (mm) REVERT: A 148 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7745 (pp) REVERT: A 458 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 483 MET cc_start: 0.8008 (tmm) cc_final: 0.7450 (tmm) REVERT: A 523 MET cc_start: 0.9005 (ttt) cc_final: 0.8319 (ttp) REVERT: A 541 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7397 (tmm) REVERT: A 567 TRP cc_start: 0.8966 (p-90) cc_final: 0.8397 (p-90) REVERT: B 131 MET cc_start: 0.8584 (mmm) cc_final: 0.7346 (mmm) REVERT: B 155 HIS cc_start: 0.8653 (t70) cc_final: 0.8280 (t70) REVERT: B 199 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8157 (mm-30) REVERT: B 253 PHE cc_start: 0.8365 (m-10) cc_final: 0.7926 (m-80) REVERT: B 413 TYR cc_start: 0.8517 (m-80) cc_final: 0.8053 (m-80) REVERT: B 481 MET cc_start: 0.8533 (tpp) cc_final: 0.8011 (ttt) REVERT: B 492 ILE cc_start: 0.8963 (tp) cc_final: 0.8685 (tp) REVERT: B 496 MET cc_start: 0.8811 (tpp) cc_final: 0.8562 (tpp) REVERT: B 523 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7824 (ttp) REVERT: B 541 MET cc_start: 0.8546 (tmm) cc_final: 0.7960 (tmm) REVERT: B 568 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 636 MET cc_start: 0.9133 (tpp) cc_final: 0.8888 (tpp) outliers start: 33 outliers final: 26 residues processed: 153 average time/residue: 0.1483 time to fit residues: 35.4497 Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 109 ASN 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 259 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL 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 89 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 545 PHE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 0.0170 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 overall best weight: 3.1824 ------------------------------------------------------------------------------- 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 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099247 restraints weight = 17522.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102377 restraints weight = 9331.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104492 restraints weight = 6212.422| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9071 Z= 0.307 Angle : 0.731 11.477 12286 Z= 0.361 Chirality : 0.046 0.375 1424 Planarity : 0.004 0.039 1519 Dihedral : 7.019 86.299 1353 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.95 % Allowed : 29.21 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.25), residues: 1114 helix: -0.41 (0.24), residues: 506 sheet: -4.69 (0.62), residues: 24 loop : -2.75 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.005 0.001 HIS A 630 PHE 0.017 0.002 PHE A 506 TYR 0.024 0.002 TYR B 463 ARG 0.003 0.000 ARG A 96 *********************** 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 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9458 (pt) cc_final: 0.9117 (mm) REVERT: A 127 ASP cc_start: 0.8763 (t0) cc_final: 0.8515 (t0) REVERT: A 148 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7830 (pp) REVERT: A 458 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8344 (mm-30) REVERT: A 483 MET cc_start: 0.8151 (tmm) cc_final: 0.7573 (tmm) REVERT: A 567 TRP cc_start: 0.9007 (p-90) cc_final: 0.8425 (p-90) REVERT: B 128 ASP cc_start: 0.8209 (m-30) cc_final: 0.7980 (p0) REVERT: B 155 HIS cc_start: 0.8723 (t70) cc_final: 0.8268 (t70) REVERT: B 199 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B 253 PHE cc_start: 0.8417 (m-10) cc_final: 0.7964 (m-80) REVERT: B 413 TYR cc_start: 0.8632 (m-80) cc_final: 0.8089 (m-80) REVERT: B 492 ILE cc_start: 0.8980 (tp) cc_final: 0.8695 (tp) REVERT: B 523 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7699 (ttp) REVERT: B 541 MET cc_start: 0.8646 (tmm) cc_final: 0.8390 (tmm) REVERT: B 568 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9116 (tt) outliers start: 38 outliers final: 31 residues processed: 161 average time/residue: 0.1420 time to fit residues: 35.5534 Evaluate side-chains 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 109 ASN 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 194 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE 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 63 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 LEU 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 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 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 557 ASN B 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105037 restraints weight = 17177.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108394 restraints weight = 8968.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110593 restraints weight = 5875.166| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9071 Z= 0.177 Angle : 0.697 13.415 12286 Z= 0.337 Chirality : 0.044 0.368 1424 Planarity : 0.004 0.039 1519 Dihedral : 6.684 73.517 1353 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.12 % Allowed : 30.56 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.25), residues: 1114 helix: -0.21 (0.24), residues: 510 sheet: -4.40 (0.68), residues: 24 loop : -2.74 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.005 0.001 HIS B 267 PHE 0.019 0.001 PHE B 506 TYR 0.033 0.002 TYR A 645 ARG 0.003 0.000 ARG B 147 ********************** 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 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9481 (pt) cc_final: 0.9163 (mm) REVERT: A 148 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7938 (pp) REVERT: A 483 MET cc_start: 0.7957 (tmm) cc_final: 0.7427 (tmm) REVERT: A 523 MET cc_start: 0.8827 (tmm) cc_final: 0.8496 (ttp) REVERT: B 128 ASP cc_start: 0.8155 (m-30) cc_final: 0.7897 (p0) REVERT: B 131 MET cc_start: 0.8585 (mmm) cc_final: 0.7292 (mmm) REVERT: B 155 HIS cc_start: 0.8614 (t70) cc_final: 0.8083 (t70) REVERT: B 199 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 253 PHE cc_start: 0.8333 (m-10) cc_final: 0.7917 (m-80) REVERT: B 413 TYR cc_start: 0.8480 (m-80) cc_final: 0.8037 (m-80) REVERT: B 481 MET cc_start: 0.8391 (tpp) cc_final: 0.7851 (ttt) REVERT: B 492 ILE cc_start: 0.8886 (tp) cc_final: 0.8595 (tp) REVERT: B 523 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8570 (tmm) REVERT: B 541 MET cc_start: 0.8369 (tmm) cc_final: 0.7924 (tmm) REVERT: B 568 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9016 (tt) REVERT: B 636 MET cc_start: 0.9092 (tpp) cc_final: 0.8792 (tpp) outliers start: 30 outliers final: 25 residues processed: 157 average time/residue: 0.1517 time to fit residues: 36.9460 Evaluate side-chains 155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 109 ASN 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 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE 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 B residue 36 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE 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 93 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 10 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5954 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.136260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105382 restraints weight = 17198.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108748 restraints weight = 9018.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110961 restraints weight = 5926.346| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9071 Z= 0.167 Angle : 0.679 13.241 12286 Z= 0.328 Chirality : 0.044 0.373 1424 Planarity : 0.004 0.038 1519 Dihedral : 6.502 71.088 1353 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.91 % Allowed : 30.15 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.26), residues: 1114 helix: 0.09 (0.25), residues: 500 sheet: -4.17 (0.77), residues: 24 loop : -2.60 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.006 0.001 HIS B 155 PHE 0.021 0.001 PHE B 506 TYR 0.030 0.001 TYR A 645 ARG 0.003 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.36 seconds wall clock time: 42 minutes 48.30 seconds (2568.30 seconds total)