Starting phenix.real_space_refine on Wed Mar 4 15:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lpe_23479/03_2026/7lpe_23479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lpe_23479/03_2026/7lpe_23479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lpe_23479/03_2026/7lpe_23479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lpe_23479/03_2026/7lpe_23479.map" model { file = "/net/cci-nas-00/data/ceres_data/7lpe_23479/03_2026/7lpe_23479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lpe_23479/03_2026/7lpe_23479.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.048 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 76 5.16 5 C 9072 2.51 5 N 2216 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13844 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3376 Classifications: {'peptide': 486} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 162} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 473} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 780 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'HIS:plan': 6, 'GLU:plan': 20, 'ARG:plan': 13, 'ASN:plan1': 8, 'TYR:plan': 3, 'PHE:plan': 7, 'GLN:plan1': 6, 'ASP:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 334 Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'4DY': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B, A, D Time building chain proxies: 2.76, per 1000 atoms: 0.20 Number of scatterers: 13844 At special positions: 0 Unit cell: (117.549, 118.608, 104.841, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 8 15.00 O 2472 8.00 N 2216 7.00 C 9072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 733.8 milliseconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 73.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 213 through 220 removed outlier: 3.699A pdb=" N VAL C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.972A pdb=" N HIS C 364 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.722A pdb=" N ASP C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 removed outlier: 3.783A pdb=" N GLY C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 510 removed outlier: 4.498A pdb=" N PHE C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 removed outlier: 4.074A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.594A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 Processing helix chain 'C' and resid 559 through 575 removed outlier: 4.283A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.962A pdb=" N MET C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 4.041A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.702A pdb=" N LEU C 662 " --> pdb=" O VAL C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 712 removed outlier: 3.681A pdb=" N ASN C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 4.084A pdb=" N LYS C 718 " --> pdb=" O LYS C 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 213 through 220 removed outlier: 3.699A pdb=" N VAL B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.972A pdb=" N HIS B 364 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.723A pdb=" N ASP B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 removed outlier: 3.783A pdb=" N GLY B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.499A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 removed outlier: 4.074A pdb=" N SER B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.595A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 559 through 575 removed outlier: 4.283A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 removed outlier: 3.962A pdb=" N MET B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 4.042A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.702A pdb=" N LEU B 662 " --> pdb=" O VAL B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 712 removed outlier: 3.681A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 4.084A pdb=" N LYS B 718 " --> pdb=" O LYS B 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.699A pdb=" N VAL A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.972A pdb=" N HIS A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.722A pdb=" N ASP A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.783A pdb=" N GLY A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 4.498A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 removed outlier: 4.074A pdb=" N SER A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.595A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 559 through 575 removed outlier: 4.284A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 3.963A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 4.042A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.701A pdb=" N LEU A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 712 removed outlier: 3.680A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 4.083A pdb=" N LYS A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'D' and resid 213 through 220 removed outlier: 3.699A pdb=" N VAL D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 355 Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.973A pdb=" N HIS D 364 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.722A pdb=" N ASP D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 removed outlier: 3.782A pdb=" N GLY D 492 " --> pdb=" O PHE D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 510 removed outlier: 4.498A pdb=" N PHE D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 removed outlier: 4.074A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.594A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 559 through 575 removed outlier: 4.284A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.962A pdb=" N MET D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 4.040A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.702A pdb=" N LEU D 662 " --> pdb=" O VAL D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 712 removed outlier: 3.681A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 4.083A pdb=" N LYS D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.592A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.593A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.592A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 725 through 730 removed outlier: 4.453A pdb=" N GLN A 727 " --> pdb=" O ARG A 739 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG A 739 " --> pdb=" O GLN A 727 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.592A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 729 through 730 1001 hydrogen bonds defined for protein. 2898 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: 2.23 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2160 1.30 - 1.43: 3899 1.43 - 1.55: 7867 1.55 - 1.68: 62 1.68 - 1.81: 136 Bond restraints: 14124 Sorted by residual: bond pdb=" C25 LBN C1001 " pdb=" O5 LBN C1001 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C25 LBN B1001 " pdb=" O5 LBN B1001 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C25 LBN D1001 " pdb=" O5 LBN D1001 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C25 LBN A1001 " pdb=" O5 LBN A1001 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C34 LBN C1001 " pdb=" O7 LBN C1001 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 14119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 18147 2.41 - 4.82: 897 4.82 - 7.23: 167 7.23 - 9.64: 53 9.64 - 12.05: 16 Bond angle restraints: 19280 Sorted by residual: angle pdb=" CB MET D 547 " pdb=" CG MET D 547 " pdb=" SD MET D 547 " ideal model delta sigma weight residual 112.70 100.97 11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB MET B 547 " pdb=" CG MET B 547 " pdb=" SD MET B 547 " ideal model delta sigma weight residual 112.70 100.99 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB MET C 547 " pdb=" CG MET C 547 " pdb=" SD MET C 547 " ideal model delta sigma weight residual 112.70 101.01 11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB MET A 547 " pdb=" CG MET A 547 " pdb=" SD MET A 547 " ideal model delta sigma weight residual 112.70 101.04 11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" N TYR A 653 " pdb=" CA TYR A 653 " pdb=" C TYR A 653 " ideal model delta sigma weight residual 110.28 115.98 -5.70 1.48e+00 4.57e-01 1.48e+01 ... (remaining 19275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 7942 33.90 - 67.80: 202 67.80 - 101.70: 4 101.70 - 135.61: 4 135.61 - 169.51: 16 Dihedral angle restraints: 8168 sinusoidal: 2468 harmonic: 5700 Sorted by residual: dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.10 59.10 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.10 59.10 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CB CYS C 386 " pdb=" SG CYS C 386 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.10 59.10 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 8165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1780 0.068 - 0.136: 407 0.136 - 0.205: 77 0.205 - 0.273: 8 0.273 - 0.341: 4 Chirality restraints: 2276 Sorted by residual: chirality pdb=" C20 6OU D1002 " pdb=" C19 6OU D1002 " pdb=" C21 6OU D1002 " pdb=" O30 6OU D1002 " both_signs ideal model delta sigma weight residual False 2.35 2.69 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C20 6OU B1002 " pdb=" C19 6OU B1002 " pdb=" C21 6OU B1002 " pdb=" O30 6OU B1002 " both_signs ideal model delta sigma weight residual False 2.35 2.68 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C20 6OU C1002 " pdb=" C19 6OU C1002 " pdb=" C21 6OU C1002 " pdb=" O30 6OU C1002 " both_signs ideal model delta sigma weight residual False 2.35 2.68 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2273 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 547 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C MET D 547 " -0.078 2.00e-02 2.50e+03 pdb=" O MET D 547 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY D 548 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 547 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C MET A 547 " -0.077 2.00e-02 2.50e+03 pdb=" O MET A 547 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY A 548 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 547 " -0.022 2.00e-02 2.50e+03 4.47e-02 1.99e+01 pdb=" C MET B 547 " 0.077 2.00e-02 2.50e+03 pdb=" O MET B 547 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY B 548 " -0.026 2.00e-02 2.50e+03 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2175 2.75 - 3.29: 14886 3.29 - 3.83: 23199 3.83 - 4.36: 25288 4.36 - 4.90: 42867 Nonbonded interactions: 108415 Sorted by model distance: nonbonded pdb=" O THR A 670 " pdb=" CD2 LEU A 675 " model vdw 2.219 3.460 nonbonded pdb=" O THR C 670 " pdb=" CD2 LEU C 675 " model vdw 2.219 3.460 nonbonded pdb=" O THR D 670 " pdb=" CD2 LEU D 675 " model vdw 2.220 3.460 nonbonded pdb=" O THR B 670 " pdb=" CD2 LEU B 675 " model vdw 2.220 3.460 nonbonded pdb=" O GLY A 485 " pdb=" OG SER A 520 " model vdw 2.275 3.040 ... (remaining 108410 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'B' selection = chain 'A' selection = chain 'D' } 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=0.50 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: 1.240 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.280 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 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 : 0.011 0.128 14128 Z= 0.523 Angle : 1.292 12.050 19288 Z= 0.689 Chirality : 0.062 0.341 2276 Planarity : 0.007 0.045 2420 Dihedral : 17.198 169.506 4484 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1912 helix: -0.23 (0.13), residues: 1240 sheet: -2.84 (0.55), residues: 76 loop : -0.63 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.003 ARG A 355 TYR 0.039 0.005 TYR B 511 PHE 0.047 0.004 PHE D 649 TRP 0.042 0.005 TRP B 697 HIS 0.000 0.000 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.01107 (14124) covalent geometry : angle 1.28962 (19280) SS BOND : bond 0.00175 ( 4) SS BOND : angle 4.31678 ( 8) hydrogen bonds : bond 0.15885 ( 1001) hydrogen bonds : angle 6.82520 ( 2898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 TYR cc_start: 0.8233 (t80) cc_final: 0.7948 (t80) REVERT: C 399 ILE cc_start: 0.9433 (mm) cc_final: 0.9201 (tt) REVERT: C 440 VAL cc_start: 0.9198 (t) cc_final: 0.8933 (p) REVERT: C 568 MET cc_start: 0.7922 (mtt) cc_final: 0.7539 (mtp) REVERT: C 571 LYS cc_start: 0.8790 (tppt) cc_final: 0.8296 (mptt) REVERT: C 581 MET cc_start: 0.6998 (tpt) cc_final: 0.6488 (tpt) REVERT: C 678 LEU cc_start: 0.7826 (tm) cc_final: 0.7530 (tm) REVERT: B 399 ILE cc_start: 0.9359 (mm) cc_final: 0.9051 (tt) REVERT: B 541 MET cc_start: 0.8748 (tmm) cc_final: 0.8509 (tmm) REVERT: B 551 ASN cc_start: 0.7472 (t0) cc_final: 0.7226 (t0) REVERT: B 559 PHE cc_start: 0.5946 (m-80) cc_final: 0.5683 (t80) REVERT: B 568 MET cc_start: 0.8018 (mtt) cc_final: 0.7752 (mtm) REVERT: B 703 ILE cc_start: 0.9734 (mm) cc_final: 0.9529 (mm) REVERT: A 309 TYR cc_start: 0.7963 (t80) cc_final: 0.7761 (t80) REVERT: A 399 ILE cc_start: 0.9387 (mm) cc_final: 0.9050 (tt) REVERT: A 440 VAL cc_start: 0.9161 (t) cc_final: 0.8958 (p) REVERT: A 523 MET cc_start: 0.9004 (tpt) cc_final: 0.8718 (tpt) REVERT: A 559 PHE cc_start: 0.5978 (m-80) cc_final: 0.5677 (t80) REVERT: A 568 MET cc_start: 0.8044 (mtt) cc_final: 0.7612 (mtm) REVERT: A 703 ILE cc_start: 0.9683 (mm) cc_final: 0.9482 (mm) REVERT: D 399 ILE cc_start: 0.9367 (mm) cc_final: 0.9122 (tt) REVERT: D 440 VAL cc_start: 0.9210 (t) cc_final: 0.8947 (p) REVERT: D 551 ASN cc_start: 0.7542 (t0) cc_final: 0.7334 (t0) REVERT: D 568 MET cc_start: 0.7946 (mtt) cc_final: 0.7609 (mtp) REVERT: D 581 MET cc_start: 0.6689 (tpt) cc_final: 0.6133 (tpt) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.0955 time to fit residues: 53.1605 Evaluate side-chains 236 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 40.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 393 ASN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.191882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.139634 restraints weight = 21724.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.141657 restraints weight = 15711.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.143034 restraints weight = 9066.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.144522 restraints weight = 7812.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.146552 restraints weight = 6293.637| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14128 Z= 0.166 Angle : 0.684 11.028 19288 Z= 0.356 Chirality : 0.040 0.161 2276 Planarity : 0.004 0.029 2420 Dihedral : 17.098 170.053 2316 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.94 % Allowed : 11.44 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1912 helix: 0.67 (0.14), residues: 1256 sheet: -3.12 (0.48), residues: 100 loop : -0.44 (0.31), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 701 TYR 0.021 0.002 TYR A 487 PHE 0.029 0.002 PHE A 496 TRP 0.021 0.002 TRP B 697 HIS 0.012 0.007 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00341 (14124) covalent geometry : angle 0.68326 (19280) SS BOND : bond 0.00365 ( 4) SS BOND : angle 1.54180 ( 8) hydrogen bonds : bond 0.05120 ( 1001) hydrogen bonds : angle 5.10046 ( 2898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 275 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9420 (mm) cc_final: 0.9156 (tt) REVERT: C 439 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7107 (t80) REVERT: C 551 ASN cc_start: 0.7951 (t0) cc_final: 0.7220 (t0) REVERT: C 552 MET cc_start: 0.8849 (tpp) cc_final: 0.8331 (ttm) REVERT: C 568 MET cc_start: 0.7796 (mtt) cc_final: 0.7477 (mtm) REVERT: C 581 MET cc_start: 0.6986 (tpt) cc_final: 0.6450 (tpt) REVERT: C 682 MET cc_start: 0.6562 (mtp) cc_final: 0.6202 (mtp) REVERT: B 399 ILE cc_start: 0.9321 (mm) cc_final: 0.9047 (tt) REVERT: B 439 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6951 (t80) REVERT: B 541 MET cc_start: 0.8368 (tmm) cc_final: 0.8110 (tmm) REVERT: B 551 ASN cc_start: 0.7927 (t0) cc_final: 0.7466 (t0) REVERT: B 552 MET cc_start: 0.8659 (ttm) cc_final: 0.8137 (ttm) REVERT: B 568 MET cc_start: 0.8124 (mtt) cc_final: 0.7824 (mtm) REVERT: A 382 TYR cc_start: 0.7848 (m-80) cc_final: 0.7592 (m-80) REVERT: A 399 ILE cc_start: 0.9385 (mm) cc_final: 0.9038 (tt) REVERT: A 401 TYR cc_start: 0.8440 (m-80) cc_final: 0.8230 (m-80) REVERT: A 541 MET cc_start: 0.8424 (tmm) cc_final: 0.8080 (tmm) REVERT: A 551 ASN cc_start: 0.7839 (t0) cc_final: 0.7628 (t0) REVERT: A 552 MET cc_start: 0.8631 (ttm) cc_final: 0.8079 (ttm) REVERT: A 682 MET cc_start: 0.6441 (mtp) cc_final: 0.5975 (mtp) REVERT: A 699 LEU cc_start: 0.9713 (tp) cc_final: 0.9487 (tt) REVERT: D 399 ILE cc_start: 0.9354 (mm) cc_final: 0.9095 (tt) REVERT: D 423 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8645 (mt0) REVERT: D 541 MET cc_start: 0.8506 (tmm) cc_final: 0.8083 (tmm) REVERT: D 581 MET cc_start: 0.7032 (tpt) cc_final: 0.6464 (tpt) outliers start: 21 outliers final: 12 residues processed: 288 average time/residue: 0.1007 time to fit residues: 45.0807 Evaluate side-chains 255 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 40.0000 chunk 147 optimal weight: 50.0000 chunk 177 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.187486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.134033 restraints weight = 21738.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.136041 restraints weight = 12889.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.137388 restraints weight = 8342.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.138519 restraints weight = 6922.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.140484 restraints weight = 6074.583| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14128 Z= 0.242 Angle : 0.691 7.212 19288 Z= 0.362 Chirality : 0.041 0.225 2276 Planarity : 0.004 0.027 2420 Dihedral : 16.655 162.173 2316 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.68 % Allowed : 14.67 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1912 helix: 1.07 (0.15), residues: 1216 sheet: -3.01 (0.51), residues: 76 loop : -0.46 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 701 TYR 0.022 0.002 TYR B 511 PHE 0.028 0.002 PHE A 496 TRP 0.021 0.002 TRP D 697 HIS 0.016 0.006 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00544 (14124) covalent geometry : angle 0.69030 (19280) SS BOND : bond 0.00278 ( 4) SS BOND : angle 1.18789 ( 8) hydrogen bonds : bond 0.04477 ( 1001) hydrogen bonds : angle 5.07628 ( 2898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9364 (mm) cc_final: 0.9076 (tt) REVERT: C 439 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7204 (t80) REVERT: C 460 LEU cc_start: 0.9260 (tp) cc_final: 0.8755 (tt) REVERT: C 515 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6985 (mm) REVERT: C 523 MET cc_start: 0.8906 (tpt) cc_final: 0.8555 (tpt) REVERT: C 552 MET cc_start: 0.8890 (tpp) cc_final: 0.8519 (ttm) REVERT: C 562 MET cc_start: 0.7097 (mmm) cc_final: 0.6645 (mmt) REVERT: C 568 MET cc_start: 0.8001 (mtt) cc_final: 0.7788 (mtm) REVERT: C 646 ASP cc_start: 0.8018 (t0) cc_final: 0.7753 (t0) REVERT: B 399 ILE cc_start: 0.9345 (mm) cc_final: 0.9122 (tp) REVERT: B 439 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.7076 (t80) REVERT: B 552 MET cc_start: 0.8681 (ttm) cc_final: 0.8267 (ttm) REVERT: B 562 MET cc_start: 0.7281 (mmm) cc_final: 0.6834 (mmt) REVERT: B 646 ASP cc_start: 0.8121 (t0) cc_final: 0.7882 (t0) REVERT: B 695 ASN cc_start: 0.8990 (t0) cc_final: 0.8739 (t0) REVERT: A 399 ILE cc_start: 0.9381 (mm) cc_final: 0.9019 (tt) REVERT: A 541 MET cc_start: 0.8565 (tmm) cc_final: 0.8198 (tmm) REVERT: A 552 MET cc_start: 0.8696 (ttm) cc_final: 0.8343 (ttm) REVERT: A 646 ASP cc_start: 0.8106 (t0) cc_final: 0.7858 (t0) REVERT: D 399 ILE cc_start: 0.9384 (mm) cc_final: 0.9135 (tt) REVERT: D 515 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7123 (mm) REVERT: D 541 MET cc_start: 0.8575 (tmm) cc_final: 0.8189 (tmm) REVERT: D 552 MET cc_start: 0.8766 (ttm) cc_final: 0.8254 (ttm) REVERT: D 646 ASP cc_start: 0.8090 (t0) cc_final: 0.7818 (t0) REVERT: D 682 MET cc_start: 0.6939 (mtp) cc_final: 0.6411 (mtp) outliers start: 29 outliers final: 25 residues processed: 259 average time/residue: 0.1008 time to fit residues: 40.4605 Evaluate side-chains 252 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 40.0000 chunk 12 optimal weight: 0.5980 chunk 149 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 110.0000 chunk 8 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 168 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.186913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.134662 restraints weight = 21776.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.133985 restraints weight = 11336.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.136106 restraints weight = 9035.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.136556 restraints weight = 6785.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.137126 restraints weight = 6423.187| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14128 Z= 0.230 Angle : 0.662 7.396 19288 Z= 0.346 Chirality : 0.040 0.148 2276 Planarity : 0.003 0.031 2420 Dihedral : 16.482 166.134 2316 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.34 % Allowed : 17.16 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1912 helix: 1.29 (0.15), residues: 1224 sheet: -2.69 (0.42), residues: 100 loop : -0.36 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 474 TYR 0.016 0.002 TYR B 554 PHE 0.019 0.002 PHE C 439 TRP 0.021 0.002 TRP D 697 HIS 0.013 0.004 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00518 (14124) covalent geometry : angle 0.66170 (19280) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.80643 ( 8) hydrogen bonds : bond 0.04155 ( 1001) hydrogen bonds : angle 4.94671 ( 2898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9403 (mm) cc_final: 0.9107 (tt) REVERT: C 439 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7271 (t80) REVERT: C 460 LEU cc_start: 0.9390 (tp) cc_final: 0.8902 (tt) REVERT: C 552 MET cc_start: 0.8755 (tpp) cc_final: 0.8471 (ttm) REVERT: C 562 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6752 (mmt) REVERT: C 568 MET cc_start: 0.8001 (mtt) cc_final: 0.7653 (mtm) REVERT: C 646 ASP cc_start: 0.8108 (t0) cc_final: 0.7840 (t0) REVERT: B 399 ILE cc_start: 0.9377 (mm) cc_final: 0.9144 (tp) REVERT: B 439 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 552 MET cc_start: 0.8638 (ttm) cc_final: 0.8267 (ttm) REVERT: B 562 MET cc_start: 0.7306 (mmm) cc_final: 0.6909 (mmt) REVERT: B 646 ASP cc_start: 0.8099 (t0) cc_final: 0.7862 (t0) REVERT: A 399 ILE cc_start: 0.9393 (mm) cc_final: 0.9103 (tt) REVERT: A 515 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7029 (mm) REVERT: A 541 MET cc_start: 0.8625 (tmm) cc_final: 0.8252 (tmm) REVERT: A 552 MET cc_start: 0.8578 (ttm) cc_final: 0.8251 (ttm) REVERT: A 646 ASP cc_start: 0.8139 (t0) cc_final: 0.7893 (t0) REVERT: D 399 ILE cc_start: 0.9408 (mm) cc_final: 0.9165 (tt) REVERT: D 541 MET cc_start: 0.8646 (tmm) cc_final: 0.8251 (tmm) REVERT: D 552 MET cc_start: 0.8594 (ttm) cc_final: 0.8177 (ttm) REVERT: D 562 MET cc_start: 0.7040 (mmm) cc_final: 0.6647 (mmt) REVERT: D 646 ASP cc_start: 0.8113 (t0) cc_final: 0.7858 (t0) REVERT: D 682 MET cc_start: 0.6480 (mtp) cc_final: 0.6000 (mtp) outliers start: 47 outliers final: 34 residues processed: 251 average time/residue: 0.0966 time to fit residues: 38.0540 Evaluate side-chains 248 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 549 TRP Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 439 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 159 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.189610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.136827 restraints weight = 21851.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.139430 restraints weight = 12947.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.140009 restraints weight = 8767.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.141055 restraints weight = 7786.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.141589 restraints weight = 6331.228| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4124 r_free = 0.4124 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4124 r_free = 0.4124 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14128 Z= 0.157 Angle : 0.595 7.120 19288 Z= 0.316 Chirality : 0.038 0.139 2276 Planarity : 0.003 0.027 2420 Dihedral : 15.970 164.993 2316 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.52 % Allowed : 18.08 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1912 helix: 1.49 (0.15), residues: 1228 sheet: -2.64 (0.42), residues: 100 loop : -0.22 (0.30), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 420 TYR 0.015 0.002 TYR C 487 PHE 0.027 0.001 PHE B 496 TRP 0.027 0.002 TRP B 697 HIS 0.011 0.004 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00343 (14124) covalent geometry : angle 0.59523 (19280) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.65015 ( 8) hydrogen bonds : bond 0.03890 ( 1001) hydrogen bonds : angle 4.74777 ( 2898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9373 (mm) cc_final: 0.9086 (tt) REVERT: C 460 LEU cc_start: 0.9343 (tp) cc_final: 0.8851 (tt) REVERT: C 523 MET cc_start: 0.8947 (tpt) cc_final: 0.8552 (tpt) REVERT: C 552 MET cc_start: 0.8549 (tpp) cc_final: 0.8323 (ttm) REVERT: C 562 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6808 (mmt) REVERT: C 568 MET cc_start: 0.7969 (mtt) cc_final: 0.7590 (mtm) REVERT: C 646 ASP cc_start: 0.8146 (t0) cc_final: 0.7927 (t0) REVERT: B 399 ILE cc_start: 0.9330 (mm) cc_final: 0.9105 (tp) REVERT: B 412 MET cc_start: 0.7314 (mmt) cc_final: 0.6864 (mmt) REVERT: B 552 MET cc_start: 0.8480 (ttm) cc_final: 0.8160 (ttm) REVERT: B 562 MET cc_start: 0.7324 (mmm) cc_final: 0.6899 (mmt) REVERT: A 399 ILE cc_start: 0.9377 (mm) cc_final: 0.9047 (tt) REVERT: A 541 MET cc_start: 0.8633 (tmm) cc_final: 0.8268 (tmm) REVERT: A 552 MET cc_start: 0.8450 (ttm) cc_final: 0.8163 (ttm) REVERT: A 646 ASP cc_start: 0.8177 (t0) cc_final: 0.7931 (t0) REVERT: D 399 ILE cc_start: 0.9396 (mm) cc_final: 0.9111 (tt) REVERT: D 541 MET cc_start: 0.8638 (tmm) cc_final: 0.8243 (tmm) REVERT: D 552 MET cc_start: 0.8440 (ttm) cc_final: 0.8086 (ttm) REVERT: D 562 MET cc_start: 0.7056 (mmm) cc_final: 0.6687 (mmt) REVERT: D 682 MET cc_start: 0.6617 (mtp) cc_final: 0.6334 (mtp) outliers start: 49 outliers final: 34 residues processed: 265 average time/residue: 0.0955 time to fit residues: 39.5302 Evaluate side-chains 256 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 549 TRP Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 549 TRP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 46 optimal weight: 40.0000 chunk 163 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.189952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.136812 restraints weight = 21810.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.140029 restraints weight = 13307.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.141172 restraints weight = 8010.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.142341 restraints weight = 6926.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.143664 restraints weight = 5979.005| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14128 Z= 0.147 Angle : 0.598 7.344 19288 Z= 0.315 Chirality : 0.038 0.201 2276 Planarity : 0.003 0.027 2420 Dihedral : 15.634 163.589 2316 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.61 % Allowed : 19.46 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1912 helix: 1.66 (0.15), residues: 1232 sheet: -3.37 (0.49), residues: 60 loop : -0.31 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 420 TYR 0.014 0.001 TYR B 487 PHE 0.013 0.001 PHE C 439 TRP 0.016 0.001 TRP A 697 HIS 0.012 0.005 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00320 (14124) covalent geometry : angle 0.59714 (19280) SS BOND : bond 0.00141 ( 4) SS BOND : angle 1.75078 ( 8) hydrogen bonds : bond 0.03729 ( 1001) hydrogen bonds : angle 4.67321 ( 2898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9358 (mm) cc_final: 0.9065 (tt) REVERT: C 460 LEU cc_start: 0.9299 (tp) cc_final: 0.8808 (tt) REVERT: C 552 MET cc_start: 0.8525 (tpp) cc_final: 0.8262 (ttm) REVERT: C 562 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6704 (mmt) REVERT: C 568 MET cc_start: 0.7965 (mtt) cc_final: 0.7742 (mtm) REVERT: C 636 GLU cc_start: 0.8404 (tp30) cc_final: 0.7812 (tp30) REVERT: C 646 ASP cc_start: 0.8204 (t0) cc_final: 0.7868 (t0) REVERT: C 678 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7540 (tm) REVERT: B 399 ILE cc_start: 0.9330 (mm) cc_final: 0.9068 (tp) REVERT: B 412 MET cc_start: 0.7276 (mmt) cc_final: 0.6798 (mmt) REVERT: B 552 MET cc_start: 0.8469 (ttm) cc_final: 0.8159 (ttm) REVERT: B 562 MET cc_start: 0.7311 (mmm) cc_final: 0.6904 (mmt) REVERT: A 399 ILE cc_start: 0.9369 (mm) cc_final: 0.9049 (tt) REVERT: A 412 MET cc_start: 0.7692 (mmt) cc_final: 0.7435 (mmt) REVERT: A 541 MET cc_start: 0.8613 (tmm) cc_final: 0.8248 (tmm) REVERT: A 552 MET cc_start: 0.8446 (ttm) cc_final: 0.8142 (ttm) REVERT: A 599 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8434 (tt) REVERT: A 678 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7376 (tm) REVERT: D 399 ILE cc_start: 0.9355 (mm) cc_final: 0.9058 (tt) REVERT: D 541 MET cc_start: 0.8615 (tmm) cc_final: 0.8222 (tmm) REVERT: D 552 MET cc_start: 0.8441 (ttm) cc_final: 0.8099 (ttm) REVERT: D 562 MET cc_start: 0.7019 (mmm) cc_final: 0.6566 (mmt) REVERT: D 636 GLU cc_start: 0.8391 (tp30) cc_final: 0.7800 (tp30) REVERT: D 646 ASP cc_start: 0.8011 (t0) cc_final: 0.7738 (t0) REVERT: D 695 ASN cc_start: 0.8956 (t0) cc_final: 0.8712 (t0) outliers start: 50 outliers final: 37 residues processed: 272 average time/residue: 0.1038 time to fit residues: 44.0874 Evaluate side-chains 268 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 549 TRP Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 549 TRP Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 549 TRP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 189 optimal weight: 50.0000 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 141 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.189057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.136216 restraints weight = 21973.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.138724 restraints weight = 13055.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.139897 restraints weight = 8221.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.141029 restraints weight = 6946.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.143447 restraints weight = 6086.841| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4145 r_free = 0.4145 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14128 Z= 0.170 Angle : 0.619 13.409 19288 Z= 0.328 Chirality : 0.039 0.174 2276 Planarity : 0.003 0.027 2420 Dihedral : 15.480 162.312 2316 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.35 % Allowed : 18.54 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1912 helix: 1.71 (0.15), residues: 1228 sheet: -3.21 (0.51), residues: 60 loop : -0.32 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 474 TYR 0.014 0.001 TYR B 487 PHE 0.013 0.001 PHE B 439 TRP 0.018 0.001 TRP D 697 HIS 0.008 0.004 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00380 (14124) covalent geometry : angle 0.61585 (19280) SS BOND : bond 0.01189 ( 4) SS BOND : angle 2.99781 ( 8) hydrogen bonds : bond 0.03757 ( 1001) hydrogen bonds : angle 4.66899 ( 2898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9344 (mm) cc_final: 0.9056 (tt) REVERT: C 445 MET cc_start: 0.8219 (mmm) cc_final: 0.7743 (mmt) REVERT: C 460 LEU cc_start: 0.9286 (tp) cc_final: 0.8876 (tt) REVERT: C 523 MET cc_start: 0.8991 (tpt) cc_final: 0.8488 (tpt) REVERT: C 552 MET cc_start: 0.8564 (tpp) cc_final: 0.8309 (ttm) REVERT: C 562 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6684 (mmt) REVERT: C 568 MET cc_start: 0.7973 (mtt) cc_final: 0.7758 (mtm) REVERT: C 646 ASP cc_start: 0.8250 (t0) cc_final: 0.8045 (t0) REVERT: B 399 ILE cc_start: 0.9327 (mm) cc_final: 0.9023 (tt) REVERT: B 412 MET cc_start: 0.7291 (mmt) cc_final: 0.6888 (mmt) REVERT: B 551 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7325 (t0) REVERT: B 552 MET cc_start: 0.8417 (ttm) cc_final: 0.8123 (ttm) REVERT: B 562 MET cc_start: 0.7341 (mmm) cc_final: 0.6885 (mmt) REVERT: A 399 ILE cc_start: 0.9383 (mm) cc_final: 0.9049 (tt) REVERT: A 445 MET cc_start: 0.8184 (mmm) cc_final: 0.7689 (mmt) REVERT: A 541 MET cc_start: 0.8592 (tmm) cc_final: 0.8226 (tmm) REVERT: A 552 MET cc_start: 0.8445 (ttm) cc_final: 0.8143 (ttm) REVERT: A 599 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8402 (tt) REVERT: D 399 ILE cc_start: 0.9359 (mm) cc_final: 0.9056 (tt) REVERT: D 541 MET cc_start: 0.8606 (tmm) cc_final: 0.8208 (tmm) REVERT: D 552 MET cc_start: 0.8472 (ttm) cc_final: 0.8130 (ttm) REVERT: D 562 MET cc_start: 0.7140 (mmm) cc_final: 0.6670 (mmt) REVERT: D 568 MET cc_start: 0.7904 (mtm) cc_final: 0.7568 (mtm) REVERT: D 636 GLU cc_start: 0.8363 (tp30) cc_final: 0.7830 (tp30) REVERT: D 646 ASP cc_start: 0.8037 (t0) cc_final: 0.7692 (t0) REVERT: D 695 ASN cc_start: 0.8950 (t0) cc_final: 0.8712 (t0) outliers start: 58 outliers final: 45 residues processed: 272 average time/residue: 0.0988 time to fit residues: 42.1738 Evaluate side-chains 272 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 549 TRP Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 549 TRP Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 549 TRP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 163 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 97 optimal weight: 50.0000 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.190800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.138529 restraints weight = 21672.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.141994 restraints weight = 12449.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.142962 restraints weight = 7625.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144251 restraints weight = 6581.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.145176 restraints weight = 5645.353| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4174 r_free = 0.4174 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4174 r_free = 0.4174 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14128 Z= 0.137 Angle : 0.615 12.376 19288 Z= 0.321 Chirality : 0.038 0.212 2276 Planarity : 0.003 0.027 2420 Dihedral : 15.245 159.282 2316 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.43 % Allowed : 20.11 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1912 helix: 1.78 (0.15), residues: 1232 sheet: -3.38 (0.60), residues: 40 loop : -0.38 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 701 TYR 0.014 0.001 TYR D 565 PHE 0.009 0.001 PHE C 438 TRP 0.027 0.002 TRP B 697 HIS 0.008 0.003 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00298 (14124) covalent geometry : angle 0.61139 (19280) SS BOND : bond 0.00859 ( 4) SS BOND : angle 3.32897 ( 8) hydrogen bonds : bond 0.03706 ( 1001) hydrogen bonds : angle 4.57585 ( 2898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9317 (mm) cc_final: 0.9051 (tt) REVERT: C 437 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8109 (t0) REVERT: C 460 LEU cc_start: 0.9293 (tp) cc_final: 0.8874 (tt) REVERT: C 552 MET cc_start: 0.8435 (tpp) cc_final: 0.8197 (ttm) REVERT: C 562 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6777 (mmm) REVERT: C 568 MET cc_start: 0.7953 (mtt) cc_final: 0.7552 (mtm) REVERT: C 636 GLU cc_start: 0.8317 (tp30) cc_final: 0.7689 (tp30) REVERT: C 646 ASP cc_start: 0.8115 (t0) cc_final: 0.7778 (t0) REVERT: B 399 ILE cc_start: 0.9283 (mm) cc_final: 0.8968 (tt) REVERT: B 412 MET cc_start: 0.7251 (mmt) cc_final: 0.6838 (mmt) REVERT: B 445 MET cc_start: 0.8188 (mmm) cc_final: 0.7671 (mmt) REVERT: B 515 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7158 (mm) REVERT: B 551 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7059 (t0) REVERT: B 552 MET cc_start: 0.8329 (ttm) cc_final: 0.8038 (ttm) REVERT: B 562 MET cc_start: 0.7253 (mmm) cc_final: 0.6727 (mmt) REVERT: A 399 ILE cc_start: 0.9371 (mm) cc_final: 0.9010 (tt) REVERT: A 412 MET cc_start: 0.7702 (mmt) cc_final: 0.7429 (mmt) REVERT: A 445 MET cc_start: 0.8156 (mmm) cc_final: 0.7653 (mmt) REVERT: A 541 MET cc_start: 0.8614 (tmm) cc_final: 0.8256 (tmm) REVERT: A 552 MET cc_start: 0.8382 (ttm) cc_final: 0.8101 (ttm) REVERT: A 599 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8356 (tt) REVERT: D 399 ILE cc_start: 0.9341 (mm) cc_final: 0.9043 (tt) REVERT: D 412 MET cc_start: 0.7560 (mmt) cc_final: 0.7218 (mmt) REVERT: D 541 MET cc_start: 0.8585 (tmm) cc_final: 0.8190 (tmm) REVERT: D 552 MET cc_start: 0.8373 (ttm) cc_final: 0.8044 (ttm) REVERT: D 562 MET cc_start: 0.7113 (mmm) cc_final: 0.6618 (mmt) REVERT: D 636 GLU cc_start: 0.8292 (tp30) cc_final: 0.7701 (tp30) REVERT: D 646 ASP cc_start: 0.8036 (t0) cc_final: 0.7659 (t0) REVERT: D 678 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7439 (tm) REVERT: D 695 ASN cc_start: 0.8943 (t0) cc_final: 0.8691 (t0) outliers start: 48 outliers final: 38 residues processed: 281 average time/residue: 0.0943 time to fit residues: 41.5311 Evaluate side-chains 278 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 549 TRP Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 99 optimal weight: 40.0000 chunk 107 optimal weight: 0.0170 chunk 110 optimal weight: 0.0270 chunk 175 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 60 optimal weight: 40.0000 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.192486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.140675 restraints weight = 21747.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.139260 restraints weight = 10623.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.142226 restraints weight = 7518.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.142611 restraints weight = 5661.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.143184 restraints weight = 5452.849| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4126 r_free = 0.4126 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4126 r_free = 0.4126 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14128 Z= 0.139 Angle : 0.635 12.854 19288 Z= 0.328 Chirality : 0.039 0.212 2276 Planarity : 0.003 0.028 2420 Dihedral : 15.019 156.053 2316 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.61 % Allowed : 20.57 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1912 helix: 1.80 (0.15), residues: 1232 sheet: -3.11 (0.65), residues: 40 loop : -0.40 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 701 TYR 0.014 0.001 TYR B 627 PHE 0.023 0.001 PHE D 496 TRP 0.023 0.001 TRP A 697 HIS 0.008 0.003 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00303 (14124) covalent geometry : angle 0.63199 (19280) SS BOND : bond 0.00795 ( 4) SS BOND : angle 3.01269 ( 8) hydrogen bonds : bond 0.03690 ( 1001) hydrogen bonds : angle 4.52109 ( 2898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9413 (mm) cc_final: 0.9120 (tt) REVERT: C 412 MET cc_start: 0.7480 (mmt) cc_final: 0.7185 (mmt) REVERT: C 437 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8240 (t0) REVERT: C 460 LEU cc_start: 0.9476 (tp) cc_final: 0.9203 (tt) REVERT: C 523 MET cc_start: 0.8933 (tpt) cc_final: 0.8391 (tpt) REVERT: C 552 MET cc_start: 0.8455 (tpp) cc_final: 0.8161 (ttm) REVERT: C 562 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6609 (mmm) REVERT: C 568 MET cc_start: 0.7915 (mtt) cc_final: 0.7584 (mtm) REVERT: C 636 GLU cc_start: 0.8122 (tp30) cc_final: 0.7665 (tp30) REVERT: C 646 ASP cc_start: 0.8041 (t0) cc_final: 0.7645 (t0) REVERT: B 399 ILE cc_start: 0.9392 (mm) cc_final: 0.9050 (tt) REVERT: B 408 ASN cc_start: 0.6410 (p0) cc_final: 0.6005 (p0) REVERT: B 412 MET cc_start: 0.7558 (mmt) cc_final: 0.7133 (mmt) REVERT: B 445 MET cc_start: 0.8343 (mmm) cc_final: 0.7827 (mmt) REVERT: B 515 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6890 (mm) REVERT: B 551 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.6872 (t0) REVERT: B 552 MET cc_start: 0.8361 (ttm) cc_final: 0.8072 (ttm) REVERT: B 562 MET cc_start: 0.7041 (mmm) cc_final: 0.6507 (mmt) REVERT: B 599 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8397 (tt) REVERT: A 399 ILE cc_start: 0.9448 (mm) cc_final: 0.9077 (tt) REVERT: A 412 MET cc_start: 0.7939 (mmt) cc_final: 0.7611 (mmt) REVERT: A 445 MET cc_start: 0.8302 (mmm) cc_final: 0.7814 (mmt) REVERT: A 541 MET cc_start: 0.8587 (tmm) cc_final: 0.8229 (tmm) REVERT: A 552 MET cc_start: 0.8342 (ttm) cc_final: 0.8030 (ttm) REVERT: A 562 MET cc_start: 0.7004 (mmm) cc_final: 0.6545 (mmt) REVERT: A 599 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8306 (tt) REVERT: D 399 ILE cc_start: 0.9457 (mm) cc_final: 0.9173 (tt) REVERT: D 541 MET cc_start: 0.8632 (tmm) cc_final: 0.8265 (tmm) REVERT: D 552 MET cc_start: 0.8403 (ttm) cc_final: 0.8076 (ttm) REVERT: D 562 MET cc_start: 0.6926 (mmm) cc_final: 0.6486 (mmt) REVERT: D 636 GLU cc_start: 0.8157 (tp30) cc_final: 0.7599 (tp30) REVERT: D 646 ASP cc_start: 0.7935 (t0) cc_final: 0.7529 (t0) REVERT: D 695 ASN cc_start: 0.9104 (t0) cc_final: 0.8843 (t0) outliers start: 50 outliers final: 40 residues processed: 288 average time/residue: 0.0953 time to fit residues: 42.9249 Evaluate side-chains 284 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 549 TRP Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 549 TRP Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 549 TRP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 5.9990 chunk 56 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.191695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.138429 restraints weight = 21584.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.140691 restraints weight = 11147.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.142013 restraints weight = 7375.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.143012 restraints weight = 6698.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.145059 restraints weight = 5434.053| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14128 Z= 0.146 Angle : 0.648 11.731 19288 Z= 0.337 Chirality : 0.040 0.216 2276 Planarity : 0.003 0.028 2420 Dihedral : 14.867 154.099 2316 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.61 % Allowed : 21.86 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1912 helix: 1.74 (0.15), residues: 1232 sheet: -2.99 (0.66), residues: 40 loop : -0.41 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 455 TYR 0.013 0.001 TYR B 565 PHE 0.027 0.001 PHE B 496 TRP 0.021 0.001 TRP D 697 HIS 0.007 0.003 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00325 (14124) covalent geometry : angle 0.64559 (19280) SS BOND : bond 0.00756 ( 4) SS BOND : angle 2.89592 ( 8) hydrogen bonds : bond 0.03671 ( 1001) hydrogen bonds : angle 4.56268 ( 2898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9375 (mm) cc_final: 0.9078 (tt) REVERT: C 412 MET cc_start: 0.7495 (mmt) cc_final: 0.7160 (mmt) REVERT: C 437 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8180 (t0) REVERT: C 460 LEU cc_start: 0.9404 (tp) cc_final: 0.9114 (tt) REVERT: C 552 MET cc_start: 0.8472 (tpp) cc_final: 0.8140 (ttm) REVERT: C 562 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6668 (mmm) REVERT: C 636 GLU cc_start: 0.8231 (tp30) cc_final: 0.7691 (tp30) REVERT: C 646 ASP cc_start: 0.8053 (t0) cc_final: 0.7683 (t0) REVERT: B 399 ILE cc_start: 0.9355 (mm) cc_final: 0.9002 (tt) REVERT: B 408 ASN cc_start: 0.6296 (p0) cc_final: 0.5906 (p0) REVERT: B 412 MET cc_start: 0.7427 (mmt) cc_final: 0.6985 (mmt) REVERT: B 445 MET cc_start: 0.8342 (mmm) cc_final: 0.7800 (mmt) REVERT: B 496 PHE cc_start: 0.8153 (m-80) cc_final: 0.7881 (m-80) REVERT: B 515 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6848 (mm) REVERT: B 551 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.6974 (t0) REVERT: B 552 MET cc_start: 0.8349 (ttm) cc_final: 0.8053 (ttm) REVERT: B 562 MET cc_start: 0.7096 (mmm) cc_final: 0.6559 (mmt) REVERT: A 399 ILE cc_start: 0.9427 (mm) cc_final: 0.9034 (tt) REVERT: A 445 MET cc_start: 0.8296 (mmm) cc_final: 0.7800 (mmt) REVERT: A 496 PHE cc_start: 0.8253 (m-80) cc_final: 0.8052 (m-80) REVERT: A 541 MET cc_start: 0.8643 (tmm) cc_final: 0.8284 (tmm) REVERT: A 552 MET cc_start: 0.8339 (ttm) cc_final: 0.8021 (ttm) REVERT: A 562 MET cc_start: 0.7083 (mmm) cc_final: 0.6598 (mmt) REVERT: A 599 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 628 ASN cc_start: 0.7111 (m-40) cc_final: 0.6910 (p0) REVERT: D 399 ILE cc_start: 0.9423 (mm) cc_final: 0.9125 (tt) REVERT: D 412 MET cc_start: 0.7675 (mmt) cc_final: 0.7354 (mmt) REVERT: D 552 MET cc_start: 0.8396 (ttm) cc_final: 0.8058 (ttm) REVERT: D 562 MET cc_start: 0.7011 (mmm) cc_final: 0.6544 (mmt) REVERT: D 636 GLU cc_start: 0.8211 (tp30) cc_final: 0.7560 (tp30) REVERT: D 646 ASP cc_start: 0.8021 (t0) cc_final: 0.7600 (t0) REVERT: D 695 ASN cc_start: 0.8984 (t0) cc_final: 0.8751 (t0) outliers start: 50 outliers final: 44 residues processed: 272 average time/residue: 0.0968 time to fit residues: 41.4001 Evaluate side-chains 286 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 507 PHE Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 549 TRP Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 549 TRP Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 549 TRP Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 675 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 0.0370 chunk 54 optimal weight: 10.0000 chunk 185 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 133 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 40 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.192224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.138889 restraints weight = 21946.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.141293 restraints weight = 11271.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.142625 restraints weight = 7512.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.143547 restraints weight = 6829.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.145166 restraints weight = 5524.493| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14128 Z= 0.143 Angle : 0.652 11.606 19288 Z= 0.337 Chirality : 0.039 0.213 2276 Planarity : 0.003 0.028 2420 Dihedral : 14.674 152.675 2316 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.80 % Allowed : 22.23 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1912 helix: 1.74 (0.15), residues: 1232 sheet: -2.88 (0.67), residues: 40 loop : -0.39 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 474 TYR 0.033 0.001 TYR D 627 PHE 0.029 0.001 PHE D 496 TRP 0.025 0.002 TRP B 697 HIS 0.008 0.003 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00317 (14124) covalent geometry : angle 0.64923 (19280) SS BOND : bond 0.00759 ( 4) SS BOND : angle 2.79292 ( 8) hydrogen bonds : bond 0.03642 ( 1001) hydrogen bonds : angle 4.54771 ( 2898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.40 seconds wall clock time: 39 minutes 20.43 seconds (2360.43 seconds total)