Starting phenix.real_space_refine on Wed Mar 4 03:40:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qm4_4587/03_2026/6qm4_4587.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qm4_4587/03_2026/6qm4_4587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qm4_4587/03_2026/6qm4_4587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qm4_4587/03_2026/6qm4_4587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qm4_4587/03_2026/6qm4_4587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qm4_4587/03_2026/6qm4_4587.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 40 5.16 5 C 6886 2.51 5 N 1760 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10580 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5290 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 28, 'TRANS': 625} Chain breaks: 5 Restraints were copied for chains: B Time building chain proxies: 4.37, per 1000 atoms: 0.41 Number of scatterers: 10580 At special positions: 0 Unit cell: (118.404, 108.284, 106.26, 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 40 16.00 O 1894 8.00 N 1760 7.00 C 6886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 520.3 milliseconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 72.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.743A pdb=" N THR A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.890A pdb=" N HIS A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.734A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.861A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.747A pdb=" N ILE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.750A pdb=" N TYR A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.581A pdb=" N TRP A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 246 removed outlier: 4.097A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.879A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.900A pdb=" N LEU A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 358 Proline residue: A 341 - end of helix removed outlier: 3.629A pdb=" N LEU A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 392 removed outlier: 3.513A pdb=" N ASP A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 416 removed outlier: 3.708A pdb=" N THR A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 460 removed outlier: 3.878A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Proline residue: A 456 - end of helix removed outlier: 3.714A pdb=" N GLN A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 removed outlier: 3.529A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 516 removed outlier: 4.304A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.736A pdb=" N VAL A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 531 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 583 removed outlier: 3.501A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 624 removed outlier: 3.628A pdb=" N ALA A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 removed outlier: 4.207A pdb=" N ASP A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 625 through 628' Processing helix chain 'A' and resid 629 through 650 removed outlier: 3.739A pdb=" N GLU A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 4.043A pdb=" N ILE A 670 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 696 removed outlier: 3.544A pdb=" N TRP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 718 removed outlier: 3.722A pdb=" N ILE A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.744A pdb=" N THR B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.890A pdb=" N HIS B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.734A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.861A pdb=" N GLU B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.748A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.750A pdb=" N TYR B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.581A pdb=" N TRP B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 246 removed outlier: 4.097A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.880A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.900A pdb=" N LEU B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 330 through 358 Proline residue: B 341 - end of helix removed outlier: 3.629A pdb=" N LEU B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 392 removed outlier: 3.513A pdb=" N ASP B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 416 removed outlier: 3.708A pdb=" N THR B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 460 removed outlier: 3.879A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Proline residue: B 456 - end of helix removed outlier: 3.714A pdb=" N GLN B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.529A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 516 removed outlier: 4.305A pdb=" N GLU B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.735A pdb=" N VAL B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 531 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.500A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 624 removed outlier: 3.628A pdb=" N ALA B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 628 removed outlier: 4.207A pdb=" N ASP B 628 " --> pdb=" O SER B 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 628' Processing helix chain 'B' and resid 629 through 650 removed outlier: 3.739A pdb=" N GLU B 635 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 684 removed outlier: 4.043A pdb=" N ILE B 670 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 674 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 696 removed outlier: 3.544A pdb=" N TRP B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 718 removed outlier: 3.722A pdb=" N ILE B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 3.825A pdb=" N PHE A 22 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.912A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.825A pdb=" N PHE B 22 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.912A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3319 1.34 - 1.46: 2219 1.46 - 1.57: 5254 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 10858 Sorted by residual: bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.20e-02 6.94e+03 1.57e+01 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.20e-02 6.94e+03 1.56e+01 bond pdb=" N GLU A 480 " pdb=" CA GLU A 480 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.15e-02 7.56e+03 3.88e+00 bond pdb=" N GLU B 480 " pdb=" CA GLU B 480 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.72e+00 bond pdb=" C THR B 340 " pdb=" N PRO B 341 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.25e-02 6.40e+03 3.46e+00 ... (remaining 10853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 14050 2.05 - 4.10: 596 4.10 - 6.16: 56 6.16 - 8.21: 22 8.21 - 10.26: 10 Bond angle restraints: 14734 Sorted by residual: angle pdb=" C SER B 584 " pdb=" N ASN B 585 " pdb=" CA ASN B 585 " ideal model delta sigma weight residual 121.70 129.34 -7.64 1.80e+00 3.09e-01 1.80e+01 angle pdb=" C SER A 584 " pdb=" N ASN A 585 " pdb=" CA ASN A 585 " ideal model delta sigma weight residual 121.70 129.33 -7.63 1.80e+00 3.09e-01 1.80e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" CB VAL A 248 " ideal model delta sigma weight residual 112.15 106.12 6.03 1.47e+00 4.63e-01 1.68e+01 angle pdb=" N VAL B 248 " pdb=" CA VAL B 248 " pdb=" CB VAL B 248 " ideal model delta sigma weight residual 112.15 106.15 6.00 1.47e+00 4.63e-01 1.67e+01 angle pdb=" C PRO B 97 " pdb=" N HIS B 98 " pdb=" CA HIS B 98 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 ... (remaining 14729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5566 17.83 - 35.67: 662 35.67 - 53.50: 116 53.50 - 71.33: 20 71.33 - 89.17: 10 Dihedral angle restraints: 6374 sinusoidal: 2554 harmonic: 3820 Sorted by residual: dihedral pdb=" CA ASN A 138 " pdb=" C ASN A 138 " pdb=" N ALA A 139 " pdb=" CA ALA A 139 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASN B 138 " pdb=" C ASN B 138 " pdb=" N ALA B 139 " pdb=" CA ALA B 139 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA HIS A 479 " pdb=" C HIS A 479 " pdb=" N GLU A 480 " pdb=" CA GLU A 480 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 6371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1209 0.053 - 0.105: 321 0.105 - 0.158: 62 0.158 - 0.210: 16 0.210 - 0.263: 8 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CB VAL B 248 " pdb=" CA VAL B 248 " pdb=" CG1 VAL B 248 " pdb=" CG2 VAL B 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1613 not shown) Planarity restraints: 1870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 455 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO B 456 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 456 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 456 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " 0.047 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO A 456 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 402 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.038 5.00e-02 4.00e+02 ... (remaining 1867 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2762 2.77 - 3.30: 9675 3.30 - 3.84: 17763 3.84 - 4.37: 20103 4.37 - 4.90: 34166 Nonbonded interactions: 84469 Sorted by model distance: nonbonded pdb=" O TYR A 439 " pdb=" OG1 THR A 443 " model vdw 2.242 3.040 nonbonded pdb=" O TYR B 439 " pdb=" OG1 THR B 443 " model vdw 2.242 3.040 nonbonded pdb=" O MET A 701 " pdb=" OG1 THR A 704 " model vdw 2.296 3.040 nonbonded pdb=" O MET B 701 " pdb=" OG1 THR B 704 " model vdw 2.296 3.040 nonbonded pdb=" OG SER B 228 " pdb=" OG SER B 569 " model vdw 2.305 3.040 ... (remaining 84464 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.860 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.007 0.070 10858 Z= 0.335 Angle : 0.991 10.261 14734 Z= 0.581 Chirality : 0.053 0.263 1616 Planarity : 0.007 0.070 1870 Dihedral : 15.633 89.167 3894 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.94 (0.15), residues: 1284 helix: -4.16 (0.08), residues: 880 sheet: -2.98 (0.68), residues: 46 loop : -2.65 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 258 TYR 0.019 0.002 TYR A 279 PHE 0.028 0.002 PHE A 396 TRP 0.017 0.002 TRP B 210 HIS 0.006 0.002 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00739 (10858) covalent geometry : angle 0.99089 (14734) hydrogen bonds : bond 0.30203 ( 606) hydrogen bonds : angle 10.15143 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 151 HIS cc_start: 0.7770 (t70) cc_final: 0.7353 (t-90) REVERT: A 282 MET cc_start: 0.6936 (tpp) cc_final: 0.5147 (ptt) REVERT: A 313 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7479 (tm-30) REVERT: A 355 ASN cc_start: 0.9022 (t0) cc_final: 0.8720 (t0) REVERT: A 491 GLU cc_start: 0.8030 (tp30) cc_final: 0.7778 (tp30) REVERT: A 648 GLN cc_start: 0.6543 (mm110) cc_final: 0.5813 (pp30) REVERT: B 151 HIS cc_start: 0.7776 (t70) cc_final: 0.7360 (t-90) REVERT: B 282 MET cc_start: 0.6877 (tpp) cc_final: 0.5123 (ptt) REVERT: B 291 GLN cc_start: 0.5455 (tm-30) cc_final: 0.5238 (tm-30) REVERT: B 355 ASN cc_start: 0.9027 (t0) cc_final: 0.8666 (t0) REVERT: B 359 ASN cc_start: 0.7574 (m-40) cc_final: 0.7168 (m-40) REVERT: B 491 GLU cc_start: 0.8112 (tp30) cc_final: 0.7891 (tp30) REVERT: B 527 CYS cc_start: 0.7724 (t) cc_final: 0.7306 (t) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1112 time to fit residues: 35.3162 Evaluate side-chains 138 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 510 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 374 GLN B 401 HIS B 510 GLN B 633 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113945 restraints weight = 17341.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114195 restraints weight = 14226.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114941 restraints weight = 13121.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115293 restraints weight = 10669.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.115378 restraints weight = 10514.247| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10858 Z= 0.144 Angle : 0.634 7.859 14734 Z= 0.330 Chirality : 0.041 0.160 1616 Planarity : 0.005 0.051 1870 Dihedral : 4.986 18.696 1406 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.60 % Allowed : 14.74 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.20), residues: 1284 helix: -1.80 (0.14), residues: 886 sheet: -2.65 (0.68), residues: 46 loop : -1.57 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 554 TYR 0.018 0.002 TYR A 439 PHE 0.015 0.001 PHE A 216 TRP 0.019 0.002 TRP B 600 HIS 0.003 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00309 (10858) covalent geometry : angle 0.63355 (14734) hydrogen bonds : bond 0.04653 ( 606) hydrogen bonds : angle 4.75799 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 49 THR cc_start: 0.8709 (p) cc_final: 0.8500 (m) REVERT: A 151 HIS cc_start: 0.7554 (t70) cc_final: 0.7130 (t-90) REVERT: A 173 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7598 (t0) REVERT: A 289 LEU cc_start: 0.7405 (tt) cc_final: 0.7148 (mm) REVERT: A 539 ASP cc_start: 0.6954 (m-30) cc_final: 0.6713 (m-30) REVERT: A 648 GLN cc_start: 0.6521 (mm110) cc_final: 0.5803 (pp30) REVERT: B 49 THR cc_start: 0.8717 (p) cc_final: 0.8423 (m) REVERT: B 87 ASP cc_start: 0.7616 (m-30) cc_final: 0.7278 (m-30) REVERT: B 138 ASN cc_start: 0.6852 (t0) cc_final: 0.6532 (t0) REVERT: B 151 HIS cc_start: 0.7507 (t70) cc_final: 0.7104 (t-90) REVERT: B 173 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7643 (t0) REVERT: B 355 ASN cc_start: 0.9188 (t0) cc_final: 0.8715 (t0) outliers start: 18 outliers final: 10 residues processed: 187 average time/residue: 0.0954 time to fit residues: 25.7694 Evaluate side-chains 150 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS B 510 GLN B 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114205 restraints weight = 17664.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112852 restraints weight = 14389.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113977 restraints weight = 13032.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114394 restraints weight = 10692.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115027 restraints weight = 9497.534| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10858 Z= 0.128 Angle : 0.595 9.283 14734 Z= 0.301 Chirality : 0.040 0.158 1616 Planarity : 0.004 0.040 1870 Dihedral : 4.472 17.382 1406 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.02 % Allowed : 16.34 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1284 helix: -0.64 (0.16), residues: 892 sheet: -2.17 (0.77), residues: 42 loop : -1.43 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 639 TYR 0.013 0.002 TYR B 393 PHE 0.029 0.001 PHE A 315 TRP 0.018 0.001 TRP A 141 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00287 (10858) covalent geometry : angle 0.59514 (14734) hydrogen bonds : bond 0.03853 ( 606) hydrogen bonds : angle 4.17540 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 151 HIS cc_start: 0.7541 (t70) cc_final: 0.7176 (t-90) REVERT: A 289 LEU cc_start: 0.7408 (tt) cc_final: 0.7138 (mm) REVERT: A 440 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 648 GLN cc_start: 0.6741 (mm110) cc_final: 0.5916 (pp30) REVERT: B 87 ASP cc_start: 0.7841 (m-30) cc_final: 0.7470 (m-30) REVERT: B 151 HIS cc_start: 0.7501 (t70) cc_final: 0.7157 (t-90) outliers start: 34 outliers final: 24 residues processed: 182 average time/residue: 0.0920 time to fit residues: 24.7431 Evaluate side-chains 147 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111002 restraints weight = 17974.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109477 restraints weight = 15728.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110594 restraints weight = 15055.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110876 restraints weight = 11724.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111246 restraints weight = 11298.313| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10858 Z= 0.222 Angle : 0.675 7.094 14734 Z= 0.344 Chirality : 0.044 0.164 1616 Planarity : 0.004 0.037 1870 Dihedral : 4.576 16.200 1406 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.44 % Allowed : 18.65 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.23), residues: 1284 helix: -0.30 (0.17), residues: 894 sheet: -2.23 (0.77), residues: 42 loop : -1.51 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 680 TYR 0.018 0.002 TYR A 279 PHE 0.032 0.002 PHE A 315 TRP 0.022 0.002 TRP B 141 HIS 0.004 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00510 (10858) covalent geometry : angle 0.67544 (14734) hydrogen bonds : bond 0.04153 ( 606) hydrogen bonds : angle 4.25106 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7490 (tt) cc_final: 0.7124 (mt) REVERT: A 305 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 440 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7547 (t80) REVERT: A 648 GLN cc_start: 0.6796 (mm110) cc_final: 0.5837 (pp30) REVERT: B 87 ASP cc_start: 0.7871 (m-30) cc_final: 0.7616 (m-30) REVERT: B 223 LEU cc_start: 0.7452 (tt) cc_final: 0.7114 (mt) REVERT: B 437 MET cc_start: 0.8886 (tpt) cc_final: 0.8612 (tpp) REVERT: B 443 THR cc_start: 0.7594 (p) cc_final: 0.7209 (t) REVERT: B 527 CYS cc_start: 0.6932 (t) cc_final: 0.6580 (t) outliers start: 50 outliers final: 36 residues processed: 176 average time/residue: 0.0908 time to fit residues: 23.5919 Evaluate side-chains 162 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.0010 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.144666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112320 restraints weight = 17502.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112575 restraints weight = 15079.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113872 restraints weight = 11979.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113988 restraints weight = 9612.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114239 restraints weight = 8869.052| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10858 Z= 0.139 Angle : 0.608 7.730 14734 Z= 0.306 Chirality : 0.041 0.160 1616 Planarity : 0.004 0.036 1870 Dihedral : 4.316 15.181 1406 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.91 % Allowed : 20.52 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1284 helix: 0.09 (0.17), residues: 890 sheet: -2.16 (0.79), residues: 42 loop : -1.32 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.012 0.001 TYR A 279 PHE 0.032 0.001 PHE A 315 TRP 0.017 0.001 TRP B 141 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00321 (10858) covalent geometry : angle 0.60845 (14734) hydrogen bonds : bond 0.03590 ( 606) hydrogen bonds : angle 3.99663 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 437 MET cc_start: 0.8813 (tpt) cc_final: 0.8181 (tpt) REVERT: A 440 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7501 (t80) REVERT: B 173 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7454 (t0) REVERT: B 443 THR cc_start: 0.7662 (p) cc_final: 0.7314 (t) REVERT: B 531 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8243 (t0) outliers start: 44 outliers final: 33 residues processed: 180 average time/residue: 0.0915 time to fit residues: 24.3156 Evaluate side-chains 164 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 156 ASN ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 42 GLN B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111771 restraints weight = 17732.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110422 restraints weight = 15992.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111125 restraints weight = 15671.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111790 restraints weight = 12702.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111859 restraints weight = 12430.105| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10858 Z= 0.173 Angle : 0.636 8.482 14734 Z= 0.320 Chirality : 0.042 0.183 1616 Planarity : 0.004 0.034 1870 Dihedral : 4.310 15.497 1406 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.80 % Allowed : 21.31 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1284 helix: 0.22 (0.17), residues: 892 sheet: -2.25 (0.78), residues: 42 loop : -1.26 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 697 TYR 0.015 0.002 TYR A 279 PHE 0.032 0.002 PHE A 315 TRP 0.019 0.001 TRP B 141 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00401 (10858) covalent geometry : angle 0.63629 (14734) hydrogen bonds : bond 0.03683 ( 606) hydrogen bonds : angle 4.03669 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 440 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7508 (t80) REVERT: B 443 THR cc_start: 0.7760 (p) cc_final: 0.7487 (t) outliers start: 54 outliers final: 38 residues processed: 175 average time/residue: 0.0944 time to fit residues: 24.2976 Evaluate side-chains 160 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 117 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 42 GLN B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.145244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112834 restraints weight = 17387.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113075 restraints weight = 14915.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114308 restraints weight = 11996.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114387 restraints weight = 9843.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114661 restraints weight = 8949.825| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10858 Z= 0.132 Angle : 0.625 9.467 14734 Z= 0.311 Chirality : 0.041 0.199 1616 Planarity : 0.004 0.035 1870 Dihedral : 4.193 15.251 1406 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.44 % Allowed : 22.29 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.24), residues: 1284 helix: 0.49 (0.17), residues: 884 sheet: -2.27 (0.77), residues: 42 loop : -1.05 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 249 TYR 0.015 0.001 TYR B 188 PHE 0.034 0.001 PHE A 315 TRP 0.017 0.001 TRP A 141 HIS 0.003 0.000 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00302 (10858) covalent geometry : angle 0.62461 (14734) hydrogen bonds : bond 0.03457 ( 606) hydrogen bonds : angle 3.89049 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 384 MET cc_start: 0.7554 (mtt) cc_final: 0.6750 (mtt) REVERT: A 437 MET cc_start: 0.8819 (tpt) cc_final: 0.8102 (tpt) REVERT: A 440 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7465 (t80) REVERT: B 173 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7434 (t0) REVERT: B 290 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7323 (tt) REVERT: B 384 MET cc_start: 0.7379 (mtt) cc_final: 0.7154 (mtm) REVERT: B 443 THR cc_start: 0.7818 (p) cc_final: 0.7487 (t) outliers start: 50 outliers final: 38 residues processed: 173 average time/residue: 0.0884 time to fit residues: 22.8345 Evaluate side-chains 163 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 42 GLN B 156 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111754 restraints weight = 17491.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112073 restraints weight = 15021.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113236 restraints weight = 12052.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113308 restraints weight = 9747.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113394 restraints weight = 8862.510| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10858 Z= 0.158 Angle : 0.634 10.270 14734 Z= 0.318 Chirality : 0.042 0.202 1616 Planarity : 0.004 0.034 1870 Dihedral : 4.175 14.593 1406 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.80 % Allowed : 21.85 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1284 helix: 0.54 (0.17), residues: 884 sheet: -2.31 (0.77), residues: 42 loop : -0.98 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 697 TYR 0.014 0.001 TYR A 188 PHE 0.034 0.002 PHE A 315 TRP 0.019 0.001 TRP B 141 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00367 (10858) covalent geometry : angle 0.63359 (14734) hydrogen bonds : bond 0.03527 ( 606) hydrogen bonds : angle 3.91600 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 440 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 693 MET cc_start: 0.7660 (mmt) cc_final: 0.7155 (mmm) REVERT: B 290 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7309 (tt) REVERT: B 305 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8289 (tt) REVERT: B 440 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7540 (t80) REVERT: B 527 CYS cc_start: 0.7383 (t) cc_final: 0.7075 (t) outliers start: 54 outliers final: 41 residues processed: 174 average time/residue: 0.0899 time to fit residues: 23.5314 Evaluate side-chains 165 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 42 GLN B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112281 restraints weight = 17372.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112672 restraints weight = 14956.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113812 restraints weight = 11846.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113880 restraints weight = 9756.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113968 restraints weight = 8806.450| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10858 Z= 0.148 Angle : 0.657 10.989 14734 Z= 0.326 Chirality : 0.042 0.260 1616 Planarity : 0.004 0.034 1870 Dihedral : 4.175 15.322 1406 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.71 % Allowed : 22.47 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1284 helix: 0.60 (0.17), residues: 884 sheet: -2.35 (0.76), residues: 42 loop : -0.95 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 697 TYR 0.014 0.001 TYR B 188 PHE 0.036 0.001 PHE A 315 TRP 0.020 0.001 TRP B 141 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00341 (10858) covalent geometry : angle 0.65722 (14734) hydrogen bonds : bond 0.03478 ( 606) hydrogen bonds : angle 3.89642 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 437 MET cc_start: 0.8824 (tpt) cc_final: 0.7995 (tpt) REVERT: A 440 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7339 (t80) REVERT: A 507 MET cc_start: 0.8846 (mmp) cc_final: 0.8603 (mmp) REVERT: A 693 MET cc_start: 0.7589 (mmt) cc_final: 0.7131 (mmm) REVERT: B 290 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7352 (tt) REVERT: B 305 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8261 (tt) REVERT: B 384 MET cc_start: 0.7494 (mtt) cc_final: 0.7228 (ptp) REVERT: B 440 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7517 (t80) REVERT: B 507 MET cc_start: 0.8851 (mmp) cc_final: 0.8613 (mmp) REVERT: B 527 CYS cc_start: 0.7289 (t) cc_final: 0.6974 (t) outliers start: 53 outliers final: 44 residues processed: 172 average time/residue: 0.0898 time to fit residues: 23.1784 Evaluate side-chains 168 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 119 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 78 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 42 GLN B 156 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114622 restraints weight = 17244.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114825 restraints weight = 14768.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115738 restraints weight = 11833.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116012 restraints weight = 10061.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116132 restraints weight = 8902.964| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10858 Z= 0.123 Angle : 0.646 11.519 14734 Z= 0.318 Chirality : 0.041 0.229 1616 Planarity : 0.004 0.035 1870 Dihedral : 4.096 14.560 1406 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.17 % Allowed : 22.82 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1284 helix: 0.76 (0.17), residues: 884 sheet: -2.26 (0.77), residues: 42 loop : -0.87 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 249 TYR 0.015 0.001 TYR A 188 PHE 0.038 0.001 PHE A 315 TRP 0.018 0.001 TRP B 141 HIS 0.002 0.000 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00282 (10858) covalent geometry : angle 0.64630 (14734) hydrogen bonds : bond 0.03306 ( 606) hydrogen bonds : angle 3.80037 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8079 (tt) REVERT: A 437 MET cc_start: 0.8802 (tpt) cc_final: 0.7959 (tpt) REVERT: A 440 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7344 (t80) REVERT: A 507 MET cc_start: 0.8846 (mmp) cc_final: 0.8616 (mmp) REVERT: B 173 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7380 (t0) REVERT: B 305 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8153 (tt) REVERT: B 440 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7497 (t80) REVERT: B 507 MET cc_start: 0.8857 (mmp) cc_final: 0.8628 (mmp) REVERT: B 556 ASP cc_start: 0.7285 (t0) cc_final: 0.7034 (t0) outliers start: 47 outliers final: 36 residues processed: 164 average time/residue: 0.0841 time to fit residues: 21.1191 Evaluate side-chains 157 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 0.0970 chunk 28 optimal weight: 10.0000 chunk 129 optimal weight: 0.5980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 42 GLN B 156 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114486 restraints weight = 17231.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115011 restraints weight = 14603.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116172 restraints weight = 11846.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116265 restraints weight = 9388.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116458 restraints weight = 8664.776| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10858 Z= 0.129 Angle : 0.643 11.369 14734 Z= 0.319 Chirality : 0.040 0.189 1616 Planarity : 0.004 0.035 1870 Dihedral : 4.051 14.502 1406 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.35 % Allowed : 22.38 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1284 helix: 0.86 (0.17), residues: 884 sheet: -2.27 (0.76), residues: 42 loop : -0.86 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 697 TYR 0.015 0.001 TYR A 188 PHE 0.037 0.001 PHE A 315 TRP 0.020 0.001 TRP B 141 HIS 0.003 0.000 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00298 (10858) covalent geometry : angle 0.64252 (14734) hydrogen bonds : bond 0.03235 ( 606) hydrogen bonds : angle 3.76536 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.41 seconds wall clock time: 28 minutes 1.42 seconds (1681.42 seconds total)