Starting phenix.real_space_refine on Wed Sep 25 14:56:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm4_4587/09_2024/6qm4_4587.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm4_4587/09_2024/6qm4_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm4_4587/09_2024/6qm4_4587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm4_4587/09_2024/6qm4_4587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm4_4587/09_2024/6qm4_4587.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm4_4587/09_2024/6qm4_4587.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 10.53, per 1000 atoms: 1.00 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: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.00 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: 2.83 Time building geometry restraints manager: 3.02 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: 0.00 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: 1.010 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.680 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- 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= 0.463 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 : 3.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP B 210 HIS 0.006 0.002 HIS B 611 PHE 0.028 0.002 PHE A 396 TYR 0.019 0.002 TYR A 279 ARG 0.004 0.001 ARG B 258 *********************** 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 fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.140 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: 0.7777 (tp30) REVERT: A 648 GLN cc_start: 0.6543 (mm110) cc_final: 0.5814 (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: 0.7573 (m-40) cc_final: 0.7168 (m-40) REVERT: B 491 GLU cc_start: 0.8112 (tp30) cc_final: 0.7890 (tp30) REVERT: B 527 CYS cc_start: 0.7724 (t) cc_final: 0.7308 (t) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2538 time to fit residues: 79.5236 Evaluate side-chains 138 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2591 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= 0.181 Angle : 0.629 7.822 14734 Z= 0.327 Chirality : 0.041 0.163 1616 Planarity : 0.005 0.051 1870 Dihedral : 4.964 18.702 1406 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.33 % Allowed : 15.19 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.20), residues: 1284 helix: -1.82 (0.14), residues: 886 sheet: -2.60 (0.69), residues: 46 loop : -1.59 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 600 HIS 0.003 0.001 HIS B 479 PHE 0.014 0.001 PHE A 216 TYR 0.018 0.002 TYR A 439 ARG 0.005 0.000 ARG B 554 *********************** 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 191 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 138 ASN cc_start: 0.7288 (t0) cc_final: 0.7062 (t0) REVERT: A 151 HIS cc_start: 0.7672 (t70) cc_final: 0.7200 (t-90) REVERT: A 170 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7605 (mp0) REVERT: A 173 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7615 (t0) REVERT: A 289 LEU cc_start: 0.7125 (tt) cc_final: 0.6814 (mm) REVERT: A 491 GLU cc_start: 0.8282 (tp30) cc_final: 0.8079 (tp30) REVERT: A 539 ASP cc_start: 0.7145 (m-30) cc_final: 0.6851 (m-30) REVERT: A 566 SER cc_start: 0.8968 (t) cc_final: 0.8690 (p) REVERT: A 648 GLN cc_start: 0.6600 (mm110) cc_final: 0.5806 (pp30) REVERT: B 87 ASP cc_start: 0.8147 (m-30) cc_final: 0.7791 (m-30) REVERT: B 138 ASN cc_start: 0.7137 (t0) cc_final: 0.6794 (t0) REVERT: B 151 HIS cc_start: 0.7623 (t70) cc_final: 0.7154 (t-90) REVERT: B 170 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7586 (mp0) REVERT: B 173 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7669 (t0) REVERT: B 355 ASN cc_start: 0.9130 (t0) cc_final: 0.8643 (t0) REVERT: B 387 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.8014 (m-80) outliers start: 15 outliers final: 7 residues processed: 187 average time/residue: 0.2198 time to fit residues: 58.5264 Evaluate side-chains 151 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 387 PHE 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 65 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 366 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10858 Z= 0.283 Angle : 0.645 9.064 14734 Z= 0.331 Chirality : 0.042 0.176 1616 Planarity : 0.005 0.044 1870 Dihedral : 4.715 17.114 1406 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.73 % Allowed : 16.70 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.22), residues: 1284 helix: -0.74 (0.16), residues: 894 sheet: -2.26 (0.77), residues: 42 loop : -1.59 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 141 HIS 0.003 0.001 HIS B 611 PHE 0.031 0.002 PHE A 315 TYR 0.016 0.002 TYR A 279 ARG 0.004 0.000 ARG B 639 *********************** 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 fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 170 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7747 (mp0) REVERT: A 312 LEU cc_start: 0.9174 (mt) cc_final: 0.8969 (mt) REVERT: A 648 GLN cc_start: 0.6821 (mm110) cc_final: 0.5883 (pp30) REVERT: B 79 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8108 (mm-40) REVERT: B 87 ASP cc_start: 0.8454 (m-30) cc_final: 0.8108 (m-30) REVERT: B 138 ASN cc_start: 0.7349 (t0) cc_final: 0.7030 (t0) REVERT: B 170 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7729 (mp0) REVERT: B 173 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7768 (t0) REVERT: B 437 MET cc_start: 0.8700 (tpt) cc_final: 0.8399 (tpp) outliers start: 42 outliers final: 32 residues processed: 183 average time/residue: 0.2115 time to fit residues: 55.3273 Evaluate side-chains 166 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 153 HIS Chi-restraints excluded: chain A residue 173 ASP 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 449 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 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 334 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 440 PHE 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 116 optimal weight: 0.0770 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 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 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10858 Z= 0.193 Angle : 0.597 7.506 14734 Z= 0.300 Chirality : 0.040 0.157 1616 Planarity : 0.004 0.039 1870 Dihedral : 4.367 16.025 1406 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.73 % Allowed : 18.21 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1284 helix: -0.11 (0.17), residues: 888 sheet: -2.20 (0.77), residues: 42 loop : -1.33 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 141 HIS 0.004 0.001 HIS A 479 PHE 0.035 0.001 PHE A 315 TYR 0.011 0.001 TYR A 279 ARG 0.003 0.000 ARG B 697 *********************** 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 187 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8039 (mt0) REVERT: A 170 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7657 (mp0) REVERT: A 305 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8210 (tt) REVERT: A 387 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: A 440 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7490 (t80) REVERT: A 648 GLN cc_start: 0.6809 (mm110) cc_final: 0.5807 (pp30) REVERT: B 79 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7999 (mm-40) REVERT: B 87 ASP cc_start: 0.8300 (m-30) cc_final: 0.8070 (m-30) REVERT: B 170 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7668 (mp0) REVERT: B 173 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7521 (t0) REVERT: B 384 MET cc_start: 0.7485 (mtt) cc_final: 0.7193 (mtt) REVERT: B 387 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (m-80) outliers start: 42 outliers final: 26 residues processed: 180 average time/residue: 0.2061 time to fit residues: 53.4074 Evaluate side-chains 160 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 PHE 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 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 305 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 387 PHE 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 104 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 31 optimal weight: 20.0000 overall best weight: 1.9224 ------------------------------------------------------------------------------- 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 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** A 633 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10858 Z= 0.256 Angle : 0.618 7.500 14734 Z= 0.313 Chirality : 0.042 0.175 1616 Planarity : 0.004 0.036 1870 Dihedral : 4.336 15.201 1406 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.17 % Allowed : 19.54 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1284 helix: 0.12 (0.17), residues: 892 sheet: -2.27 (0.77), residues: 42 loop : -1.34 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 141 HIS 0.004 0.001 HIS A 611 PHE 0.032 0.002 PHE A 315 TYR 0.015 0.002 TYR A 279 ARG 0.003 0.000 ARG B 249 *********************** 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 187 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8009 (mt0) REVERT: A 170 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7722 (mp0) REVERT: A 305 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 440 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7544 (t80) REVERT: B 170 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 173 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7573 (t0) REVERT: B 249 ARG cc_start: 0.8329 (tpm170) cc_final: 0.7536 (tpm170) REVERT: B 384 MET cc_start: 0.7462 (mtt) cc_final: 0.7215 (mtt) REVERT: B 387 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 437 MET cc_start: 0.8685 (tpt) cc_final: 0.7829 (tpt) REVERT: B 443 THR cc_start: 0.7653 (p) cc_final: 0.7273 (t) outliers start: 47 outliers final: 35 residues processed: 181 average time/residue: 0.2096 time to fit residues: 55.1378 Evaluate side-chains 174 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 PHE 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 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 274 GLU 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 387 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3773 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= 0.217 Angle : 0.609 8.504 14734 Z= 0.306 Chirality : 0.041 0.172 1616 Planarity : 0.004 0.036 1870 Dihedral : 4.232 14.981 1406 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.17 % Allowed : 20.69 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1284 helix: 0.37 (0.17), residues: 888 sheet: -2.28 (0.77), residues: 42 loop : -1.21 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 141 HIS 0.003 0.001 HIS A 611 PHE 0.032 0.001 PHE A 315 TYR 0.014 0.002 TYR A 188 ARG 0.003 0.000 ARG B 249 *********************** 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 185 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7665 (mp0) REVERT: A 305 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 440 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7563 (t80) REVERT: B 79 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8099 (mt0) REVERT: B 170 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7701 (mp0) REVERT: B 173 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7473 (t0) REVERT: B 223 LEU cc_start: 0.7644 (tt) cc_final: 0.7274 (mt) REVERT: B 312 LEU cc_start: 0.9131 (mt) cc_final: 0.8813 (mt) REVERT: B 387 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: B 437 MET cc_start: 0.8693 (tpt) cc_final: 0.7790 (tpt) REVERT: B 443 THR cc_start: 0.7618 (p) cc_final: 0.7283 (t) REVERT: B 556 ASP cc_start: 0.7632 (t0) cc_final: 0.7093 (t0) outliers start: 47 outliers final: 36 residues processed: 179 average time/residue: 0.2092 time to fit residues: 54.2035 Evaluate side-chains 167 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 PHE 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 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 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 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 387 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3802 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= 0.290 Angle : 0.650 9.450 14734 Z= 0.329 Chirality : 0.042 0.196 1616 Planarity : 0.004 0.035 1870 Dihedral : 4.308 15.664 1406 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.24 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1284 helix: 0.35 (0.17), residues: 888 sheet: -2.48 (0.73), residues: 42 loop : -1.19 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 141 HIS 0.004 0.001 HIS A 611 PHE 0.031 0.002 PHE A 315 TYR 0.016 0.002 TYR A 279 ARG 0.003 0.000 ARG A 554 *********************** 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 195 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 136 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7716 (mp0) REVERT: A 282 MET cc_start: 0.6826 (tpp) cc_final: 0.6616 (tpp) REVERT: A 305 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8164 (tt) REVERT: A 387 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: A 440 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 79 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8085 (mt0) REVERT: B 170 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7719 (mp0) REVERT: B 290 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6854 (tt) REVERT: B 312 LEU cc_start: 0.9212 (mt) cc_final: 0.8949 (mt) REVERT: B 384 MET cc_start: 0.7679 (mtt) cc_final: 0.7344 (mpt) outliers start: 59 outliers final: 42 residues processed: 189 average time/residue: 0.2148 time to fit residues: 60.9722 Evaluate side-chains 175 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 244 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 387 PHE 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 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 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 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 410 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 50 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** 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 B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10858 Z= 0.208 Angle : 0.623 10.424 14734 Z= 0.311 Chirality : 0.041 0.193 1616 Planarity : 0.004 0.036 1870 Dihedral : 4.190 14.879 1406 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.09 % Allowed : 22.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1284 helix: 0.53 (0.17), residues: 886 sheet: -2.41 (0.74), residues: 42 loop : -0.94 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 141 HIS 0.003 0.001 HIS A 611 PHE 0.031 0.001 PHE A 315 TYR 0.015 0.002 TYR A 188 ARG 0.002 0.000 ARG A 554 *********************** 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 181 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7624 (mp0) REVERT: A 305 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 387 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: A 440 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7481 (t80) REVERT: A 506 GLU cc_start: 0.8282 (tp30) cc_final: 0.8054 (tp30) REVERT: A 507 MET cc_start: 0.8862 (mmp) cc_final: 0.8632 (mmp) REVERT: B 79 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8057 (mt0) REVERT: B 170 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7648 (mp0) REVERT: B 290 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6819 (tt) REVERT: B 305 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8243 (tt) REVERT: B 312 LEU cc_start: 0.9206 (mt) cc_final: 0.8950 (mt) REVERT: B 384 MET cc_start: 0.7571 (mtt) cc_final: 0.7337 (mtt) REVERT: B 387 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: B 440 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7326 (t80) REVERT: B 556 ASP cc_start: 0.7635 (t0) cc_final: 0.7376 (t0) outliers start: 46 outliers final: 35 residues processed: 175 average time/residue: 0.2039 time to fit residues: 52.0575 Evaluate side-chains 169 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 173 ASP Chi-restraints excluded: chain A residue 187 PHE 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 387 PHE 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 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 65 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 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 387 PHE Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 410 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 606 ILE 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 109 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 0.0030 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 0.0040 overall best weight: 0.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 374 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10858 Z= 0.166 Angle : 0.601 11.039 14734 Z= 0.300 Chirality : 0.040 0.179 1616 Planarity : 0.004 0.037 1870 Dihedral : 4.033 14.562 1406 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.09 % Allowed : 23.00 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1284 helix: 0.75 (0.17), residues: 886 sheet: -2.75 (0.66), residues: 44 loop : -0.91 (0.37), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 141 HIS 0.002 0.000 HIS B 611 PHE 0.033 0.001 PHE A 315 TYR 0.016 0.001 TYR A 188 ARG 0.004 0.000 ARG B 45 *********************** 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 191 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 145 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8015 (tt) REVERT: A 387 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: A 437 MET cc_start: 0.8634 (tpt) cc_final: 0.7659 (tpt) REVERT: A 440 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7493 (t80) REVERT: A 506 GLU cc_start: 0.8270 (tp30) cc_final: 0.8033 (tp30) REVERT: A 507 MET cc_start: 0.8883 (mmp) cc_final: 0.8663 (mmp) REVERT: A 510 GLN cc_start: 0.8313 (tt0) cc_final: 0.8037 (tt0) REVERT: B 79 GLN cc_start: 0.8247 (mm-40) cc_final: 0.8031 (mt0) REVERT: B 170 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7585 (mp0) REVERT: B 249 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7196 (tpm170) REVERT: B 305 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (tt) REVERT: B 384 MET cc_start: 0.7381 (mtt) cc_final: 0.7091 (mtt) REVERT: B 387 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: B 440 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7292 (t80) outliers start: 46 outliers final: 33 residues processed: 185 average time/residue: 0.1922 time to fit residues: 53.1119 Evaluate side-chains 168 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 387 PHE 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 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 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 387 PHE 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 606 ILE 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 75 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 129 optimal weight: 0.2980 chunk 119 optimal weight: 0.0670 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10858 Z= 0.189 Angle : 0.628 11.276 14734 Z= 0.312 Chirality : 0.040 0.189 1616 Planarity : 0.004 0.037 1870 Dihedral : 3.986 14.090 1406 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.17 % Allowed : 23.27 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1284 helix: 0.85 (0.17), residues: 890 sheet: -2.70 (0.66), residues: 44 loop : -0.92 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 141 HIS 0.003 0.000 HIS B 611 PHE 0.030 0.001 PHE A 315 TYR 0.015 0.001 TYR B 188 ARG 0.003 0.000 ARG A 249 ********************** 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 180 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7700 (tt) cc_final: 0.7431 (mt) REVERT: A 305 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8017 (tt) REVERT: A 387 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: A 440 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7551 (t80) REVERT: A 506 GLU cc_start: 0.8256 (tp30) cc_final: 0.8013 (tp30) REVERT: B 170 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7571 (mp0) REVERT: B 249 ARG cc_start: 0.7880 (tpp-160) cc_final: 0.7155 (tpm170) REVERT: B 305 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (tt) REVERT: B 384 MET cc_start: 0.7671 (mtt) cc_final: 0.7341 (mtt) REVERT: B 387 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: B 440 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7293 (t80) outliers start: 47 outliers final: 37 residues processed: 173 average time/residue: 0.1910 time to fit residues: 49.6492 Evaluate side-chains 167 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 387 PHE 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 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 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 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 362 THR Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 387 PHE 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 606 ILE 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 31 optimal weight: 8.9990 chunk 95 optimal weight: 0.0070 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 43 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.3560 ------------------------------------------------------------------------------- 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 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 156 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113609 restraints weight = 17279.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112677 restraints weight = 15376.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113986 restraints weight = 13712.130| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4198 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= 0.213 Angle : 0.629 11.163 14734 Z= 0.315 Chirality : 0.041 0.172 1616 Planarity : 0.004 0.036 1870 Dihedral : 3.996 13.535 1406 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.44 % Allowed : 22.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1284 helix: 0.88 (0.17), residues: 890 sheet: -2.63 (0.67), residues: 44 loop : -0.89 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 141 HIS 0.003 0.001 HIS B 611 PHE 0.029 0.001 PHE A 315 TYR 0.014 0.002 TYR A 393 ARG 0.004 0.000 ARG A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.24 seconds wall clock time: 37 minutes 1.49 seconds (2221.49 seconds total)