Starting phenix.real_space_refine on Fri Jul 3 14:11:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lpe_23479/07_2026/7lpe_23479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lpe_23479/07_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_23479/07_2026/7lpe_23479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lpe_23479/07_2026/7lpe_23479.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lpe_23479/07_2026/7lpe_23479.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lpe_23479/07_2026/7lpe_23479.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lpe_23479/07_2026/7lpe_23479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lpe_23479/07_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-6108/lib/python3.11/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: 37 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: 2.45, per 1000 atoms: 0.18 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: 1.38 Conformation dependent library (CDL) restraints added in 749.1 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: 0.40 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: 2.24 Time building geometry restraints manager: 1.82 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: 7906 33.90 - 67.80: 170 67.80 - 101.70: 4 101.70 - 135.61: 4 135.61 - 169.51: 8 Dihedral angle restraints: 8092 sinusoidal: 2392 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 8089 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: 0.05 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 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 : 15.395 169.506 4408 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/Z covalent geometry : bond 0.01107 / 0.52 (14124) covalent geometry : angle 1.28962 / 0.69 (19280) SS BOND : bond 0.00175 / 0.09 ( 4) SS BOND : angle 4.31678 / 2.52 ( 8) hydrogen bonds : bond 0.15885 / 11.54 ( 1001) hydrogen bonds : angle 6.82520 / 4.99 ( 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 : 0.430 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: 0.0896 time to fit residues: 49.8811 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 : 0.505 ------------------------------------------------------------------------------- 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... 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 = 0.191921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.139252 restraints weight = 21723.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.141313 restraints weight = 11948.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.142928 restraints weight = 8489.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.143971 restraints weight = 6982.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.144037 restraints weight = 6189.000| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4155 r_free = 0.4155 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14128 Z= 0.170 Angle : 0.685 10.895 19288 Z= 0.356 Chirality : 0.039 0.162 2276 Planarity : 0.004 0.030 2420 Dihedral : 14.528 169.727 2240 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.85 % Allowed : 11.53 % 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: 0.11 (0.20), residues: 1912 helix: 0.67 (0.14), residues: 1256 sheet: -3.15 (0.48), residues: 100 loop : -0.43 (0.31), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 701 TYR 0.021 0.002 TYR A 487 PHE 0.030 0.002 PHE A 496 TRP 0.021 0.002 TRP C 697 HIS 0.012 0.007 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (14124) covalent geometry : angle 0.68418 / 0.36 (19280) SS BOND : bond 0.00380 / 0.19 ( 4) SS BOND : angle 1.59323 / 0.93 ( 8) hydrogen bonds : bond 0.05109 / 3.66 ( 1001) hydrogen bonds : angle 5.08503 / 3.75 ( 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: 20 poor density : 276 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 351 TYR cc_start: 0.8901 (t80) cc_final: 0.8697 (t80) REVERT: C 399 ILE cc_start: 0.9444 (mm) cc_final: 0.9181 (tt) REVERT: C 439 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7155 (t80) REVERT: C 551 ASN cc_start: 0.7818 (t0) cc_final: 0.7077 (t0) REVERT: C 552 MET cc_start: 0.8848 (tpp) cc_final: 0.8385 (ttm) REVERT: C 553 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8232 (tt) REVERT: C 568 MET cc_start: 0.7790 (mtt) cc_final: 0.7537 (mtm) REVERT: C 581 MET cc_start: 0.6960 (tpt) cc_final: 0.6444 (tpt) REVERT: C 682 MET cc_start: 0.6541 (mtp) cc_final: 0.6153 (mtp) REVERT: B 399 ILE cc_start: 0.9342 (mm) cc_final: 0.9067 (tt) REVERT: B 439 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 541 MET cc_start: 0.8381 (tmm) cc_final: 0.8120 (tmm) REVERT: B 551 ASN cc_start: 0.7971 (t0) cc_final: 0.7545 (t0) REVERT: B 552 MET cc_start: 0.8657 (ttm) cc_final: 0.8150 (ttm) REVERT: B 568 MET cc_start: 0.8141 (mtt) cc_final: 0.7849 (mtm) REVERT: A 382 TYR cc_start: 0.7930 (m-80) cc_final: 0.7666 (m-80) REVERT: A 399 ILE cc_start: 0.9404 (mm) cc_final: 0.9056 (tt) REVERT: A 401 TYR cc_start: 0.8473 (m-80) cc_final: 0.8262 (m-80) REVERT: A 541 MET cc_start: 0.8441 (tmm) cc_final: 0.8060 (tmm) REVERT: A 551 ASN cc_start: 0.7791 (t0) cc_final: 0.7520 (t0) REVERT: A 552 MET cc_start: 0.8621 (ttm) cc_final: 0.8070 (ttm) REVERT: A 682 MET cc_start: 0.6482 (mtp) cc_final: 0.6041 (mtp) REVERT: D 399 ILE cc_start: 0.9375 (mm) cc_final: 0.9120 (tt) REVERT: D 541 MET cc_start: 0.8511 (tmm) cc_final: 0.8080 (tmm) REVERT: D 571 LYS cc_start: 0.8963 (tppt) cc_final: 0.8456 (mptt) REVERT: D 581 MET cc_start: 0.7017 (tpt) cc_final: 0.6464 (tpt) outliers start: 20 outliers final: 11 residues processed: 289 average time/residue: 0.0866 time to fit residues: 38.7965 Evaluate side-chains 254 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 50.0000 chunk 147 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 628 ASN ** 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 ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** 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 695 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 = 0.4688 r_free = 0.4688 target = 0.192980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.140219 restraints weight = 21785.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.143857 restraints weight = 13479.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.145263 restraints weight = 7774.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.146514 restraints weight = 6673.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.148170 restraints weight = 5714.521| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4199 r_free = 0.4199 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4199 r_free = 0.4199 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2675 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= 0.143 Angle : 0.595 8.027 19288 Z= 0.315 Chirality : 0.038 0.203 2276 Planarity : 0.003 0.029 2420 Dihedral : 13.922 166.494 2240 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.21 % Allowed : 13.19 % Favored : 84.59 % 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: 0.81 (0.20), residues: 1912 helix: 1.28 (0.15), residues: 1224 sheet: -2.71 (0.44), residues: 100 loop : -0.29 (0.30), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 701 TYR 0.017 0.001 TYR B 487 PHE 0.028 0.001 PHE A 496 TRP 0.024 0.002 TRP B 697 HIS 0.010 0.005 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14124) covalent geometry : angle 0.59435 / 0.32 (19280) SS BOND : bond 0.00231 / 0.12 ( 4) SS BOND : angle 1.19982 / 0.69 ( 8) hydrogen bonds : bond 0.04309 / 3.09 ( 1001) hydrogen bonds : angle 4.75884 / 3.52 ( 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 285 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9365 (mm) cc_final: 0.9090 (tt) REVERT: C 439 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7136 (t80) REVERT: C 460 LEU cc_start: 0.9176 (tp) cc_final: 0.8922 (tt) REVERT: C 523 MET cc_start: 0.8768 (tpt) cc_final: 0.8511 (tpt) REVERT: C 551 ASN cc_start: 0.7635 (t0) cc_final: 0.6574 (t0) REVERT: C 552 MET cc_start: 0.8719 (tpp) cc_final: 0.8452 (ttm) REVERT: C 568 MET cc_start: 0.7978 (mtt) cc_final: 0.7737 (mtm) REVERT: C 646 ASP cc_start: 0.7864 (t0) cc_final: 0.7633 (t0) REVERT: B 399 ILE cc_start: 0.9320 (mm) cc_final: 0.9076 (tp) REVERT: B 421 LEU cc_start: 0.9230 (tp) cc_final: 0.8835 (tp) REVERT: B 439 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6925 (t80) REVERT: B 552 MET cc_start: 0.8548 (ttm) cc_final: 0.8114 (ttm) REVERT: B 562 MET cc_start: 0.7307 (mmm) cc_final: 0.6884 (mmt) REVERT: B 682 MET cc_start: 0.6646 (mtp) cc_final: 0.6309 (mtp) REVERT: A 399 ILE cc_start: 0.9370 (mm) cc_final: 0.8990 (tt) REVERT: A 541 MET cc_start: 0.8498 (tmm) cc_final: 0.8111 (tmm) REVERT: A 552 MET cc_start: 0.8530 (ttm) cc_final: 0.8109 (ttm) REVERT: A 644 MET cc_start: 0.8842 (tpt) cc_final: 0.8532 (tpt) REVERT: A 646 ASP cc_start: 0.7950 (t0) cc_final: 0.7737 (t0) REVERT: A 682 MET cc_start: 0.6649 (mtp) cc_final: 0.6266 (mtp) REVERT: D 382 TYR cc_start: 0.8003 (m-80) cc_final: 0.7609 (m-80) REVERT: D 399 ILE cc_start: 0.9353 (mm) cc_final: 0.9056 (tt) REVERT: D 421 LEU cc_start: 0.9278 (tp) cc_final: 0.8962 (tp) REVERT: D 552 MET cc_start: 0.8623 (ttm) cc_final: 0.8198 (ttm) REVERT: D 571 LYS cc_start: 0.8936 (tppt) cc_final: 0.8360 (mptt) REVERT: D 646 ASP cc_start: 0.7971 (t0) cc_final: 0.7764 (t0) REVERT: D 682 MET cc_start: 0.6843 (mtp) cc_final: 0.6392 (mtp) outliers start: 24 outliers final: 19 residues processed: 274 average time/residue: 0.0908 time to fit residues: 38.3852 Evaluate side-chains 251 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 516 PHE 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 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 551 ASN 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 473 PHE Chi-restraints excluded: chain D residue 583 VAL 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: 30.0000 chunk 12 optimal weight: 0.1980 chunk 149 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 110.0000 chunk 8 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 143 optimal weight: 0.4980 chunk 168 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN ** C 700 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** ** 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 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN D 393 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.187625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.134733 restraints weight = 21819.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.132267 restraints weight = 12349.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.134540 restraints weight = 9772.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.134487 restraints weight = 7832.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.135565 restraints weight = 6623.882| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14128 Z= 0.236 Angle : 0.673 7.273 19288 Z= 0.350 Chirality : 0.040 0.154 2276 Planarity : 0.003 0.029 2420 Dihedral : 13.769 162.852 2240 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.98 % Allowed : 15.50 % Favored : 79.52 % 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: 0.92 (0.20), residues: 1912 helix: 1.33 (0.15), residues: 1232 sheet: -3.47 (0.48), residues: 60 loop : -0.28 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 701 TYR 0.021 0.002 TYR A 511 PHE 0.019 0.002 PHE C 369 TRP 0.020 0.002 TRP B 697 HIS 0.008 0.003 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (14124) covalent geometry : angle 0.67270 / 0.35 (19280) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 0.80792 / 0.47 ( 8) hydrogen bonds : bond 0.04145 / 2.98 ( 1001) hydrogen bonds : angle 4.96077 / 3.67 ( 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 286 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9428 (mm) cc_final: 0.9143 (tt) REVERT: C 439 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7298 (t80) REVERT: C 460 LEU cc_start: 0.9420 (tp) cc_final: 0.8944 (tt) REVERT: C 552 MET cc_start: 0.8892 (tpp) cc_final: 0.8497 (ttm) REVERT: C 562 MET cc_start: 0.7204 (mmm) cc_final: 0.6691 (mmt) REVERT: C 568 MET cc_start: 0.8101 (mtt) cc_final: 0.7885 (mtm) REVERT: C 646 ASP cc_start: 0.8025 (t0) cc_final: 0.7785 (t0) REVERT: B 399 ILE cc_start: 0.9404 (mm) cc_final: 0.9167 (tp) REVERT: B 412 MET cc_start: 0.7547 (mmt) cc_final: 0.7248 (mmt) REVERT: B 523 MET cc_start: 0.8917 (tpt) cc_final: 0.8628 (tpt) REVERT: B 552 MET cc_start: 0.8614 (ttm) cc_final: 0.8247 (ttm) REVERT: B 562 MET cc_start: 0.7406 (mmm) cc_final: 0.6998 (mmt) REVERT: B 599 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8388 (tt) REVERT: A 399 ILE cc_start: 0.9422 (mm) cc_final: 0.9097 (tt) REVERT: A 401 TYR cc_start: 0.8563 (m-80) cc_final: 0.8362 (m-80) REVERT: A 541 MET cc_start: 0.8566 (tmm) cc_final: 0.8183 (tmm) REVERT: A 552 MET cc_start: 0.8397 (ttm) cc_final: 0.8100 (ttm) REVERT: A 553 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7610 (mt) REVERT: A 562 MET cc_start: 0.7136 (mmm) cc_final: 0.6752 (mmt) REVERT: A 646 ASP cc_start: 0.8073 (t0) cc_final: 0.7816 (t0) REVERT: A 682 MET cc_start: 0.6728 (mtp) cc_final: 0.6304 (mtp) REVERT: D 399 ILE cc_start: 0.9439 (mm) cc_final: 0.9178 (tt) REVERT: D 515 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7220 (mm) REVERT: D 541 MET cc_start: 0.8638 (tmm) cc_final: 0.8280 (tmm) REVERT: D 552 MET cc_start: 0.8653 (ttm) cc_final: 0.8249 (ttm) REVERT: D 562 MET cc_start: 0.7428 (mmm) cc_final: 0.7113 (mmt) REVERT: D 646 ASP cc_start: 0.8047 (t0) cc_final: 0.7802 (t0) REVERT: D 682 MET cc_start: 0.6674 (mtp) cc_final: 0.6220 (mtp) outliers start: 54 outliers final: 41 residues processed: 264 average time/residue: 0.0886 time to fit residues: 36.4192 Evaluate side-chains 260 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 549 TRP 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 C residue 687 ASN 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 573 ILE Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE 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 516 PHE Chi-restraints excluded: chain A residue 549 TRP Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 586 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 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 573 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 159 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 437 ASN ** 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 437 ASN ** 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 628 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 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.188286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.134899 restraints weight = 21954.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.136398 restraints weight = 12503.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.138253 restraints weight = 8256.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.139236 restraints weight = 6807.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.139559 restraints weight = 6095.853| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14128 Z= 0.193 Angle : 0.624 7.156 19288 Z= 0.328 Chirality : 0.039 0.182 2276 Planarity : 0.003 0.027 2420 Dihedral : 13.476 165.561 2240 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.15 % Allowed : 17.71 % Favored : 78.14 % 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: 1.07 (0.20), residues: 1912 helix: 1.50 (0.15), residues: 1228 sheet: -3.49 (0.49), residues: 60 loop : -0.33 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 474 TYR 0.016 0.002 TYR B 487 PHE 0.019 0.002 PHE C 496 TRP 0.022 0.002 TRP B 697 HIS 0.014 0.005 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (14124) covalent geometry : angle 0.62362 / 0.33 (19280) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 0.66102 / 0.38 ( 8) hydrogen bonds : bond 0.03925 / 2.81 ( 1001) hydrogen bonds : angle 4.80199 / 3.56 ( 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 270 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9367 (mm) cc_final: 0.9064 (tt) REVERT: C 460 LEU cc_start: 0.9331 (tp) cc_final: 0.8844 (tt) REVERT: C 523 MET cc_start: 0.8925 (tpt) cc_final: 0.8473 (tpt) REVERT: C 552 MET cc_start: 0.8751 (tpp) cc_final: 0.8469 (ttm) REVERT: C 562 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6806 (mmt) REVERT: C 568 MET cc_start: 0.8135 (mtt) cc_final: 0.7924 (mtm) REVERT: C 646 ASP cc_start: 0.8168 (t0) cc_final: 0.7910 (t0) REVERT: B 399 ILE cc_start: 0.9344 (mm) cc_final: 0.9113 (tp) REVERT: B 412 MET cc_start: 0.7389 (mmt) cc_final: 0.7039 (mmt) REVERT: B 552 MET cc_start: 0.8496 (ttm) cc_final: 0.8176 (ttm) REVERT: B 562 MET cc_start: 0.7453 (mmm) cc_final: 0.7017 (mmt) REVERT: B 599 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 399 ILE cc_start: 0.9357 (mm) cc_final: 0.9043 (tt) REVERT: A 515 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7262 (mm) REVERT: A 541 MET cc_start: 0.8623 (tmm) cc_final: 0.8247 (tmm) REVERT: A 552 MET cc_start: 0.8501 (ttm) cc_final: 0.8239 (ttm) REVERT: A 562 MET cc_start: 0.7256 (mmm) cc_final: 0.6848 (mmt) REVERT: A 646 ASP cc_start: 0.8186 (t0) cc_final: 0.7955 (t0) REVERT: A 682 MET cc_start: 0.6750 (mtp) cc_final: 0.6268 (mtp) REVERT: D 399 ILE cc_start: 0.9386 (mm) cc_final: 0.9102 (tt) REVERT: D 423 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8583 (mt0) REVERT: D 515 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7329 (mm) REVERT: D 541 MET cc_start: 0.8600 (tmm) cc_final: 0.8219 (tmm) REVERT: D 552 MET cc_start: 0.8541 (ttm) cc_final: 0.8195 (ttm) REVERT: D 562 MET cc_start: 0.7388 (mmm) cc_final: 0.7059 (mmt) REVERT: D 636 GLU cc_start: 0.8454 (tp30) cc_final: 0.7983 (tp30) REVERT: D 646 ASP cc_start: 0.8128 (t0) cc_final: 0.7786 (t0) REVERT: D 682 MET cc_start: 0.6922 (mtp) cc_final: 0.6465 (mtp) outliers start: 45 outliers final: 34 residues processed: 253 average time/residue: 0.0906 time to fit residues: 35.3919 Evaluate side-chains 262 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 586 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 THR 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 573 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE 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 516 PHE 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 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 573 ILE 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: 0.9990 chunk 163 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.191472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.139370 restraints weight = 21820.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.143050 restraints weight = 13627.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.144143 restraints weight = 7944.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.145254 restraints weight = 6969.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.146184 restraints weight = 5958.438| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 0.030 14128 Z= 0.132 Angle : 0.582 7.539 19288 Z= 0.304 Chirality : 0.038 0.159 2276 Planarity : 0.003 0.027 2420 Dihedral : 13.070 163.816 2240 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.51 % Allowed : 19.28 % Favored : 77.21 % 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: 1.34 (0.20), residues: 1912 helix: 1.72 (0.15), residues: 1232 sheet: -3.32 (0.51), residues: 60 loop : -0.28 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 474 TYR 0.017 0.001 TYR B 487 PHE 0.012 0.001 PHE C 439 TRP 0.024 0.001 TRP B 697 HIS 0.014 0.005 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14124) covalent geometry : angle 0.58101 / 0.30 (19280) SS BOND : bond 0.00411 / 0.21 ( 4) SS BOND : angle 1.41946 / 1.01 ( 8) hydrogen bonds : bond 0.03688 / 2.65 ( 1001) hydrogen bonds : angle 4.57824 / 3.40 ( 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 284 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9342 (mm) cc_final: 0.9037 (tt) REVERT: C 460 LEU cc_start: 0.9252 (tp) cc_final: 0.8758 (tt) REVERT: C 562 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6683 (mmt) REVERT: C 568 MET cc_start: 0.8104 (mtt) cc_final: 0.7800 (mtm) REVERT: B 399 ILE cc_start: 0.9295 (mm) cc_final: 0.9011 (tp) REVERT: B 412 MET cc_start: 0.7193 (mmt) cc_final: 0.6686 (mmt) REVERT: B 552 MET cc_start: 0.8347 (ttm) cc_final: 0.8057 (ttm) REVERT: B 562 MET cc_start: 0.7266 (mmm) cc_final: 0.6806 (mmt) REVERT: A 399 ILE cc_start: 0.9350 (mm) cc_final: 0.9012 (tt) REVERT: A 541 MET cc_start: 0.8610 (tmm) cc_final: 0.8226 (tmm) REVERT: A 552 MET cc_start: 0.8389 (ttm) cc_final: 0.8135 (ttm) REVERT: A 562 MET cc_start: 0.7281 (mmm) cc_final: 0.6849 (mmt) REVERT: A 646 ASP cc_start: 0.8146 (t0) cc_final: 0.7922 (t0) REVERT: A 682 MET cc_start: 0.6658 (mtp) cc_final: 0.6299 (mtp) REVERT: D 399 ILE cc_start: 0.9351 (mm) cc_final: 0.9055 (tt) REVERT: D 423 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8592 (mt0) REVERT: D 515 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7381 (mm) REVERT: D 552 MET cc_start: 0.8410 (ttm) cc_final: 0.8078 (ttm) REVERT: D 562 MET cc_start: 0.7294 (mmm) cc_final: 0.6878 (mmt) REVERT: D 568 MET cc_start: 0.7710 (mtm) cc_final: 0.7203 (mtm) REVERT: D 636 GLU cc_start: 0.8317 (tp30) cc_final: 0.7783 (tp30) REVERT: D 646 ASP cc_start: 0.8061 (t0) cc_final: 0.7748 (t0) REVERT: D 682 MET cc_start: 0.6751 (mtp) cc_final: 0.6459 (mtp) REVERT: D 695 ASN cc_start: 0.8955 (t0) cc_final: 0.8729 (t0) outliers start: 38 outliers final: 30 residues processed: 270 average time/residue: 0.0840 time to fit residues: 35.3995 Evaluate side-chains 265 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 577 LEU 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 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 588 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 395 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 663 LEU 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 516 PHE Chi-restraints excluded: chain D residue 549 TRP Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 189 optimal weight: 50.0000 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** 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** B 676 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 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.192099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.140289 restraints weight = 22002.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.143233 restraints weight = 12941.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.143750 restraints weight = 8606.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.145004 restraints weight = 7556.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.147492 restraints weight = 6098.003| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4192 r_free = 0.4192 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4192 r_free = 0.4192 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 14128 Z= 0.136 Angle : 0.592 12.710 19288 Z= 0.315 Chirality : 0.038 0.234 2276 Planarity : 0.003 0.027 2420 Dihedral : 12.872 160.812 2240 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.24 % Allowed : 19.93 % Favored : 75.83 % 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: 1.42 (0.20), residues: 1912 helix: 1.81 (0.15), residues: 1232 sheet: -3.15 (0.53), residues: 60 loop : -0.32 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 420 TYR 0.015 0.001 TYR C 487 PHE 0.011 0.001 PHE C 438 TRP 0.024 0.002 TRP D 697 HIS 0.009 0.004 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (14124) covalent geometry : angle 0.58817 / 0.31 (19280) SS BOND : bond 0.00904 / 0.43 ( 4) SS BOND : angle 3.33041 / 1.77 ( 8) hydrogen bonds : bond 0.03608 / 2.60 ( 1001) hydrogen bonds : angle 4.54284 / 3.38 ( 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: 46 poor density : 247 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9339 (mm) cc_final: 0.9040 (tt) REVERT: C 437 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8084 (t0) REVERT: C 445 MET cc_start: 0.8175 (mmm) cc_final: 0.7667 (mmt) REVERT: C 460 LEU cc_start: 0.9243 (tp) cc_final: 0.8814 (tt) REVERT: C 515 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6809 (mm) REVERT: C 562 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6785 (mmm) REVERT: C 678 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7417 (tm) REVERT: B 399 ILE cc_start: 0.9314 (mm) cc_final: 0.9009 (tt) REVERT: B 412 MET cc_start: 0.7234 (mmt) cc_final: 0.6760 (mmt) REVERT: B 445 MET cc_start: 0.8140 (mmm) cc_final: 0.7619 (mmt) REVERT: B 552 MET cc_start: 0.8333 (ttm) cc_final: 0.8027 (ttm) REVERT: B 562 MET cc_start: 0.7343 (mmm) cc_final: 0.6787 (mmt) REVERT: B 599 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8145 (tt) REVERT: A 399 ILE cc_start: 0.9357 (mm) cc_final: 0.9012 (tt) REVERT: A 412 MET cc_start: 0.7701 (mmt) cc_final: 0.7453 (mmt) REVERT: A 445 MET cc_start: 0.8133 (mmm) cc_final: 0.7660 (mmt) REVERT: A 541 MET cc_start: 0.8583 (tmm) cc_final: 0.8214 (tmm) REVERT: A 552 MET cc_start: 0.8341 (ttm) cc_final: 0.8086 (ttm) REVERT: A 562 MET cc_start: 0.7250 (mmm) cc_final: 0.6797 (mmt) REVERT: A 682 MET cc_start: 0.6603 (mtp) cc_final: 0.6262 (mtp) REVERT: D 399 ILE cc_start: 0.9358 (mm) cc_final: 0.9047 (tt) REVERT: D 423 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8598 (mt0) REVERT: D 541 MET cc_start: 0.8558 (tmm) cc_final: 0.8250 (tmm) REVERT: D 552 MET cc_start: 0.8419 (ttm) cc_final: 0.8091 (ttm) REVERT: D 562 MET cc_start: 0.7356 (mmm) cc_final: 0.6858 (mmt) REVERT: D 636 GLU cc_start: 0.8281 (tp30) cc_final: 0.7731 (tp30) REVERT: D 646 ASP cc_start: 0.8033 (t0) cc_final: 0.7700 (t0) REVERT: D 682 MET cc_start: 0.6847 (mtp) cc_final: 0.6405 (mtp) REVERT: D 695 ASN cc_start: 0.8920 (t0) cc_final: 0.8687 (t0) REVERT: D 700 GLN cc_start: 0.9106 (mp10) cc_final: 0.8878 (mp10) outliers start: 46 outliers final: 33 residues processed: 275 average time/residue: 0.0891 time to fit residues: 38.3297 Evaluate side-chains 277 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 ASN 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 562 MET Chi-restraints excluded: chain C residue 577 LEU 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 678 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 577 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 663 LEU 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 551 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 663 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 163 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 146 optimal weight: 40.0000 chunk 104 optimal weight: 8.9990 chunk 53 optimal weight: 40.0000 chunk 64 optimal weight: 0.3980 chunk 97 optimal weight: 30.0000 chunk 167 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN B 676 ASN ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** 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** D 628 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.192469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.140242 restraints weight = 21862.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.143246 restraints weight = 12676.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144647 restraints weight = 7659.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.145983 restraints weight = 6514.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.146311 restraints weight = 5598.438| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4210 r_free = 0.4210 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4209 r_free = 0.4209 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14128 Z= 0.134 Angle : 0.607 12.497 19288 Z= 0.320 Chirality : 0.038 0.246 2276 Planarity : 0.003 0.031 2420 Dihedral : 12.652 157.495 2240 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.43 % Allowed : 19.74 % Favored : 75.83 % 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: 1.51 (0.20), residues: 1912 helix: 1.89 (0.15), residues: 1232 sheet: -3.02 (0.55), residues: 60 loop : -0.33 (0.28), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 474 TYR 0.017 0.001 TYR B 565 PHE 0.010 0.001 PHE C 438 TRP 0.022 0.001 TRP B 697 HIS 0.017 0.006 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14124) covalent geometry : angle 0.60354 / 0.32 (19280) SS BOND : bond 0.00833 / 0.40 ( 4) SS BOND : angle 3.41135 / 1.71 ( 8) hydrogen bonds : bond 0.03593 / 2.59 ( 1001) hydrogen bonds : angle 4.51654 / 3.36 ( 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 303 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9332 (mm) cc_final: 0.9021 (tt) REVERT: C 423 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8783 (pt0) REVERT: C 437 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8110 (t0) REVERT: C 460 LEU cc_start: 0.9280 (tp) cc_final: 0.8856 (tt) REVERT: C 562 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6679 (mmt) REVERT: C 678 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7426 (tm) REVERT: B 399 ILE cc_start: 0.9310 (mm) cc_final: 0.9009 (tt) REVERT: B 412 MET cc_start: 0.7303 (mmt) cc_final: 0.6780 (mmt) REVERT: B 445 MET cc_start: 0.8151 (mmm) cc_final: 0.7638 (mmt) REVERT: B 552 MET cc_start: 0.8294 (ttm) cc_final: 0.8002 (ttm) REVERT: B 562 MET cc_start: 0.7294 (mmm) cc_final: 0.6727 (mmt) REVERT: B 599 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 678 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7286 (tm) REVERT: A 399 ILE cc_start: 0.9378 (mm) cc_final: 0.9023 (tt) REVERT: A 445 MET cc_start: 0.8131 (mmm) cc_final: 0.7636 (mmt) REVERT: A 541 MET cc_start: 0.8640 (tmm) cc_final: 0.8273 (tmm) REVERT: A 552 MET cc_start: 0.8280 (ttm) cc_final: 0.8016 (ttm) REVERT: A 562 MET cc_start: 0.7156 (mmm) cc_final: 0.6634 (mmt) REVERT: A 682 MET cc_start: 0.6569 (mtp) cc_final: 0.6200 (mtp) REVERT: D 399 ILE cc_start: 0.9357 (mm) cc_final: 0.9050 (tt) REVERT: D 412 MET cc_start: 0.7580 (mmt) cc_final: 0.7248 (mmt) REVERT: D 423 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8645 (mt0) REVERT: D 541 MET cc_start: 0.8586 (tmm) cc_final: 0.8270 (tmm) REVERT: D 552 MET cc_start: 0.8407 (ttm) cc_final: 0.8081 (ttm) REVERT: D 562 MET cc_start: 0.7290 (mmm) cc_final: 0.6845 (mmt) REVERT: D 636 GLU cc_start: 0.8239 (tp30) cc_final: 0.7640 (tp30) REVERT: D 646 ASP cc_start: 0.7990 (t0) cc_final: 0.7666 (t0) REVERT: D 682 MET cc_start: 0.6838 (mtp) cc_final: 0.6385 (mtp) REVERT: D 695 ASN cc_start: 0.8992 (t0) cc_final: 0.8723 (t0) outliers start: 48 outliers final: 39 residues processed: 283 average time/residue: 0.0871 time to fit residues: 38.3377 Evaluate side-chains 283 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 515 LEU Chi-restraints excluded: chain C residue 516 PHE 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 588 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 678 LEU 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 577 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 678 LEU 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 551 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 663 LEU 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 628 ASN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 685 THR 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: 0.0570 chunk 180 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 99 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 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 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 = 0.4725 r_free = 0.4725 target = 0.192287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.142355 restraints weight = 21814.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.141486 restraints weight = 8950.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143911 restraints weight = 7493.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.145417 restraints weight = 5408.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.145524 restraints weight = 5021.764| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4201 r_free = 0.4201 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4201 r_free = 0.4201 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14128 Z= 0.149 Angle : 0.623 12.249 19288 Z= 0.329 Chirality : 0.039 0.243 2276 Planarity : 0.003 0.034 2420 Dihedral : 12.585 156.025 2240 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.17 % Allowed : 19.56 % Favored : 75.28 % 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: 1.50 (0.20), residues: 1912 helix: 1.88 (0.15), residues: 1232 sheet: -3.07 (0.64), residues: 40 loop : -0.44 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 420 TYR 0.024 0.001 TYR A 627 PHE 0.021 0.001 PHE D 496 TRP 0.041 0.002 TRP B 697 HIS 0.014 0.005 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14124) covalent geometry : angle 0.62003 / 0.33 (19280) SS BOND : bond 0.00803 / 0.38 ( 4) SS BOND : angle 3.03066 / 1.53 ( 8) hydrogen bonds : bond 0.03584 / 2.59 ( 1001) hydrogen bonds : angle 4.56890 / 3.41 ( 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 300 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9377 (mm) cc_final: 0.9057 (tt) REVERT: C 423 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8786 (pt0) REVERT: C 437 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8181 (t0) REVERT: C 460 LEU cc_start: 0.9392 (tp) cc_final: 0.8988 (tt) REVERT: C 515 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6663 (mm) REVERT: C 562 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6482 (mmt) REVERT: C 568 MET cc_start: 0.7704 (mtm) cc_final: 0.7473 (mtm) REVERT: B 399 ILE cc_start: 0.9339 (mm) cc_final: 0.9007 (tt) REVERT: B 412 MET cc_start: 0.7419 (mmt) cc_final: 0.6882 (mmt) REVERT: B 445 MET cc_start: 0.8296 (mmm) cc_final: 0.7797 (mmt) REVERT: B 552 MET cc_start: 0.8400 (ttm) cc_final: 0.8083 (ttm) REVERT: B 562 MET cc_start: 0.7122 (mmm) cc_final: 0.6564 (mmt) REVERT: B 599 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8164 (tt) REVERT: A 399 ILE cc_start: 0.9418 (mm) cc_final: 0.9063 (tt) REVERT: A 412 MET cc_start: 0.7852 (mmt) cc_final: 0.7567 (mmt) REVERT: A 445 MET cc_start: 0.8289 (mmm) cc_final: 0.7795 (mmt) REVERT: A 541 MET cc_start: 0.8609 (tmm) cc_final: 0.8226 (tmm) REVERT: A 552 MET cc_start: 0.8344 (ttm) cc_final: 0.8074 (ttm) REVERT: A 562 MET cc_start: 0.6976 (mmm) cc_final: 0.6495 (mmt) REVERT: A 599 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 682 MET cc_start: 0.6423 (mtp) cc_final: 0.6058 (mtp) REVERT: D 399 ILE cc_start: 0.9417 (mm) cc_final: 0.9116 (tt) REVERT: D 541 MET cc_start: 0.8590 (tmm) cc_final: 0.8242 (tmm) REVERT: D 552 MET cc_start: 0.8469 (ttm) cc_final: 0.8109 (ttm) REVERT: D 636 GLU cc_start: 0.8186 (tp30) cc_final: 0.7570 (tp30) REVERT: D 646 ASP cc_start: 0.7961 (t0) cc_final: 0.7615 (t0) REVERT: D 682 MET cc_start: 0.6511 (mtp) cc_final: 0.6117 (mtp) REVERT: D 695 ASN cc_start: 0.9064 (t0) cc_final: 0.8802 (t0) outliers start: 56 outliers final: 43 residues processed: 278 average time/residue: 0.0814 time to fit residues: 35.4305 Evaluate side-chains 291 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 515 LEU Chi-restraints excluded: chain C residue 516 PHE 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 588 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain B residue 443 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 516 PHE Chi-restraints excluded: chain B residue 549 TRP Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 663 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 549 TRP Chi-restraints excluded: chain A residue 551 ASN 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 685 THR 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 628 ASN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 7.9990 chunk 56 optimal weight: 50.0000 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 131 optimal weight: 0.2980 chunk 137 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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** D 628 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.194229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.142884 restraints weight = 21695.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.143743 restraints weight = 9652.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.145278 restraints weight = 7735.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.145624 restraints weight = 6089.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.146052 restraints weight = 5363.180| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 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 = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3969 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= 0.131 Angle : 0.632 11.962 19288 Z= 0.331 Chirality : 0.039 0.188 2276 Planarity : 0.003 0.028 2420 Dihedral : 12.458 154.295 2240 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.87 % Allowed : 21.13 % Favored : 75.00 % 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: 1.49 (0.20), residues: 1912 helix: 1.87 (0.15), residues: 1232 sheet: -2.95 (0.65), residues: 40 loop : -0.45 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 455 TYR 0.026 0.001 TYR A 627 PHE 0.028 0.001 PHE B 496 TRP 0.041 0.002 TRP B 697 HIS 0.014 0.005 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14124) covalent geometry : angle 0.62947 / 0.33 (19280) SS BOND : bond 0.00769 / 0.37 ( 4) SS BOND : angle 2.94398 / 1.48 ( 8) hydrogen bonds : bond 0.03573 / 2.58 ( 1001) hydrogen bonds : angle 4.55907 / 3.41 ( 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 306 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 ILE cc_start: 0.9408 (mm) cc_final: 0.9092 (tt) REVERT: C 423 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8726 (pt0) REVERT: C 437 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8249 (t0) REVERT: C 460 LEU cc_start: 0.9480 (tp) cc_final: 0.9099 (tt) REVERT: C 562 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6459 (mmt) REVERT: C 568 MET cc_start: 0.7714 (mtm) cc_final: 0.7075 (mtm) REVERT: B 399 ILE cc_start: 0.9370 (mm) cc_final: 0.9045 (tt) REVERT: B 412 MET cc_start: 0.7648 (mmt) cc_final: 0.7103 (mmt) REVERT: B 445 MET cc_start: 0.8297 (mmm) cc_final: 0.7809 (mmt) REVERT: B 547 MET cc_start: 0.7839 (tpp) cc_final: 0.7371 (tpp) REVERT: B 552 MET cc_start: 0.8363 (ttm) cc_final: 0.8031 (ttm) REVERT: B 562 MET cc_start: 0.6912 (mmm) cc_final: 0.6389 (mmt) REVERT: A 399 ILE cc_start: 0.9448 (mm) cc_final: 0.9089 (tt) REVERT: A 412 MET cc_start: 0.7965 (mmt) cc_final: 0.7691 (mmt) REVERT: A 445 MET cc_start: 0.8299 (mmm) cc_final: 0.7792 (mmt) REVERT: A 541 MET cc_start: 0.8634 (tmm) cc_final: 0.8248 (tmm) REVERT: A 552 MET cc_start: 0.8287 (ttm) cc_final: 0.8016 (ttm) REVERT: A 562 MET cc_start: 0.7023 (mmm) cc_final: 0.6533 (mmt) REVERT: A 599 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 682 MET cc_start: 0.6179 (mtp) cc_final: 0.5835 (mtp) REVERT: D 399 ILE cc_start: 0.9448 (mm) cc_final: 0.9165 (tt) REVERT: D 412 MET cc_start: 0.7845 (mmt) cc_final: 0.7530 (mmt) REVERT: D 423 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8621 (mt0) REVERT: D 541 MET cc_start: 0.8610 (tmm) cc_final: 0.8268 (tmm) REVERT: D 552 MET cc_start: 0.8411 (ttm) cc_final: 0.8061 (ttm) REVERT: D 646 ASP cc_start: 0.7951 (t0) cc_final: 0.7741 (t0) REVERT: D 682 MET cc_start: 0.6282 (mtp) cc_final: 0.5892 (mtp) REVERT: D 695 ASN cc_start: 0.9164 (t0) cc_final: 0.8900 (t0) outliers start: 42 outliers final: 39 residues processed: 289 average time/residue: 0.0857 time to fit residues: 38.7382 Evaluate side-chains 293 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 ASN 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 562 MET Chi-restraints excluded: chain C residue 577 LEU 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 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 516 PHE Chi-restraints excluded: chain B residue 549 TRP Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 663 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 549 TRP Chi-restraints excluded: chain A residue 551 ASN 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 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 628 ASN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 133 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 chunk 66 optimal weight: 7.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 = 0.4711 r_free = 0.4711 target = 0.191596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.140167 restraints weight = 21838.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.139980 restraints weight = 10085.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.142034 restraints weight = 7775.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.142870 restraints weight = 5814.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.143566 restraints weight = 5357.054| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.4138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14128 Z= 0.170 Angle : 0.664 11.768 19288 Z= 0.349 Chirality : 0.040 0.229 2276 Planarity : 0.003 0.028 2420 Dihedral : 12.426 154.330 2240 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.15 % Allowed : 21.68 % Favored : 74.17 % 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: 1.84 (0.15), residues: 1232 sheet: -2.87 (0.66), residues: 40 loop : -0.52 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 420 TYR 0.025 0.002 TYR A 627 PHE 0.028 0.001 PHE D 496 TRP 0.052 0.002 TRP B 697 HIS 0.012 0.004 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (14124) covalent geometry : angle 0.66180 / 0.35 (19280) SS BOND : bond 0.00747 / 0.36 ( 4) SS BOND : angle 2.85568 / 1.43 ( 8) hydrogen bonds : bond 0.03583 / 2.59 ( 1001) hydrogen bonds : angle 4.68900 / 3.50 ( 2898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.18 seconds wall clock time: 36 minutes 31.97 seconds (2191.97 seconds total)