Starting phenix.real_space_refine on Thu Sep 18 05:59:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7f_23211/09_2025/7l7f_23211.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7f_23211/09_2025/7l7f_23211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l7f_23211/09_2025/7l7f_23211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7f_23211/09_2025/7l7f_23211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l7f_23211/09_2025/7l7f_23211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7f_23211/09_2025/7l7f_23211.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9310 2.51 5 N 2428 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14542 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5809 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain: "E" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "D" Number of atoms: 5809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5809 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Time building chain proxies: 3.45, per 1000 atoms: 0.24 Number of scatterers: 14542 At special positions: 0 Unit cell: (120.93, 143.55, 138.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2724 8.00 N 2428 7.00 C 9310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " 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: 0.80 Conformation dependent library (CDL) restraints added in 586.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 49.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 21 through 53 removed outlier: 4.256A pdb=" N ALA B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 80 removed outlier: 3.995A pdb=" N ASN B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.978A pdb=" N GLU B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 173 removed outlier: 3.512A pdb=" N TRP B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 4.009A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.970A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 removed outlier: 3.824A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 303 through 318 removed outlier: 4.090A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.588A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 331' Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.940A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.715A pdb=" N ARG B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.585A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.830A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 447 removed outlier: 4.110A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.529A pdb=" N THR B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 4.336A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 530 removed outlier: 3.509A pdb=" N THR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 520 " --> pdb=" O TYR B 516 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.537A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.679A pdb=" N GLN B 552 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 581 through 588 removed outlier: 3.677A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.991A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 629 Processing helix chain 'B' and resid 636 through 660 removed outlier: 3.867A pdb=" N MET B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.517A pdb=" N VAL B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 716 removed outlier: 3.659A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 405 through 410 removed outlier: 5.765A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.863A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 80 removed outlier: 3.996A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.977A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.512A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 4.010A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.970A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.824A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 303 through 318 removed outlier: 4.089A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.587A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.941A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.715A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.585A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.830A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.110A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.530A pdb=" N THR D 453 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 466 " --> pdb=" O MET D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 4.336A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 530 removed outlier: 3.509A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.537A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.679A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.678A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.991A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 636 through 660 removed outlier: 3.867A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.517A pdb=" N VAL D 700 " --> pdb=" O PRO D 696 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 716 removed outlier: 3.659A pdb=" N ILE D 711 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 405 through 410 removed outlier: 5.764A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.077A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 673 removed outlier: 4.828A pdb=" N LYS B 619 " --> pdb=" O LEU B 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.759A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP E 398 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 512 " --> pdb=" O ASP E 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.516A pdb=" N TYR E 453 " --> pdb=" O GLN E 493 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.077A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AB1, first strand: chain 'D' and resid 670 through 673 removed outlier: 4.829A pdb=" N LYS D 619 " --> pdb=" O LEU D 725 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.759A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP F 398 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 512 " --> pdb=" O ASP F 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 452 through 454 removed outlier: 3.516A pdb=" N TYR F 453 " --> pdb=" O GLN F 493 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 493 " --> pdb=" O TYR F 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 558 hydrogen bonds defined for protein. 1596 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: 2.17 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4704 1.35 - 1.47: 3865 1.47 - 1.59: 6235 1.59 - 1.71: 0 1.71 - 1.84: 130 Bond restraints: 14934 Sorted by residual: bond pdb=" N LYS F 386 " pdb=" CA LYS F 386 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.38e-02 5.25e+03 5.63e+00 bond pdb=" N LYS E 386 " pdb=" CA LYS E 386 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.38e-02 5.25e+03 5.51e+00 bond pdb=" N TYR E 489 " pdb=" CA TYR E 489 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.38e+00 bond pdb=" C GLU D 35 " pdb=" O GLU D 35 " ideal model delta sigma weight residual 1.236 1.253 -0.017 1.22e-02 6.72e+03 1.83e+00 bond pdb=" C GLU B 35 " pdb=" O GLU B 35 " ideal model delta sigma weight residual 1.236 1.252 -0.016 1.22e-02 6.72e+03 1.79e+00 ... (remaining 14929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 19817 1.91 - 3.82: 394 3.82 - 5.73: 51 5.73 - 7.64: 0 7.64 - 9.55: 6 Bond angle restraints: 20268 Sorted by residual: angle pdb=" C GLU B 171 " pdb=" N VAL B 172 " pdb=" CA VAL B 172 " ideal model delta sigma weight residual 122.66 119.02 3.64 9.70e-01 1.06e+00 1.41e+01 angle pdb=" C GLU D 171 " pdb=" N VAL D 172 " pdb=" CA VAL D 172 " ideal model delta sigma weight residual 122.66 119.10 3.56 9.70e-01 1.06e+00 1.35e+01 angle pdb=" CA CYS E 432 " pdb=" CB CYS E 432 " pdb=" SG CYS E 432 " ideal model delta sigma weight residual 114.40 122.65 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA CYS F 432 " pdb=" CB CYS F 432 " pdb=" SG CYS F 432 " ideal model delta sigma weight residual 114.40 122.63 -8.23 2.30e+00 1.89e-01 1.28e+01 angle pdb=" N LYS F 386 " pdb=" CA LYS F 386 " pdb=" C LYS F 386 " ideal model delta sigma weight residual 113.61 108.53 5.08 1.50e+00 4.44e-01 1.15e+01 ... (remaining 20263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 7669 17.34 - 34.68: 945 34.68 - 52.02: 180 52.02 - 69.36: 46 69.36 - 86.70: 22 Dihedral angle restraints: 8862 sinusoidal: 3604 harmonic: 5258 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 11.89 81.11 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 11.90 81.10 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CA CYS E 336 " pdb=" C CYS E 336 " pdb=" N PRO E 337 " pdb=" CA PRO E 337 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1065 0.029 - 0.058: 677 0.058 - 0.087: 255 0.087 - 0.117: 107 0.117 - 0.146: 20 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA PRO B 688 " pdb=" N PRO B 688 " pdb=" C PRO B 688 " pdb=" CB PRO B 688 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA PRO D 688 " pdb=" N PRO D 688 " pdb=" C PRO D 688 " pdb=" CB PRO D 688 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 2121 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 488 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C CYS E 488 " -0.036 2.00e-02 2.50e+03 pdb=" O CYS E 488 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR E 489 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 283 " 0.029 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO D 284 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 284 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 284 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 687 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO D 688 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 688 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 688 " 0.024 5.00e-02 4.00e+02 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1106 2.73 - 3.27: 13838 3.27 - 3.82: 21239 3.82 - 4.36: 24872 4.36 - 4.90: 44383 Nonbonded interactions: 105438 Sorted by model distance: nonbonded pdb=" OE1 GLU B 435 " pdb=" NE2 HIS B 540 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLU D 435 " pdb=" NE2 HIS D 540 " model vdw 2.189 3.120 nonbonded pdb=" NE2 GLN B 524 " pdb=" N ASN B 580 " model vdw 2.266 3.200 nonbonded pdb=" NE2 GLN D 524 " pdb=" N ASN D 580 " model vdw 2.267 3.200 nonbonded pdb=" O THR E 470 " pdb=" OG1 THR E 470 " model vdw 2.295 3.040 ... (remaining 105433 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.310 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.005 0.036 14946 Z= 0.210 Angle : 0.682 9.552 20292 Z= 0.398 Chirality : 0.044 0.146 2124 Planarity : 0.005 0.043 2632 Dihedral : 15.832 86.698 5446 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.25 % Allowed : 16.35 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.17), residues: 1780 helix: -1.34 (0.17), residues: 810 sheet: -1.95 (0.54), residues: 80 loop : -3.71 (0.15), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 306 TYR 0.019 0.001 TYR B 183 PHE 0.014 0.001 PHE D 684 TRP 0.009 0.001 TRP D 594 HIS 0.004 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00465 (14934) covalent geometry : angle 0.67955 (20268) SS BOND : bond 0.00772 ( 12) SS BOND : angle 1.75468 ( 24) hydrogen bonds : bond 0.15189 ( 558) hydrogen bonds : angle 5.37054 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: B 35 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7529 (mt-10) REVERT: B 249 MET cc_start: 0.8277 (mtp) cc_final: 0.8063 (mtp) REVERT: B 557 MET cc_start: 0.9167 (tmm) cc_final: 0.8964 (tmm) REVERT: B 582 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6821 (tpt170) REVERT: E 407 VAL cc_start: 0.7864 (m) cc_final: 0.7584 (t) REVERT: E 455 LEU cc_start: 0.7359 (tp) cc_final: 0.7152 (tp) REVERT: E 474 GLN cc_start: 0.7525 (tt0) cc_final: 0.7182 (tm-30) REVERT: E 511 VAL cc_start: 0.6877 (t) cc_final: 0.6643 (p) REVERT: D 249 MET cc_start: 0.8348 (mtp) cc_final: 0.8142 (mtp) REVERT: D 349 TRP cc_start: 0.8687 (m100) cc_final: 0.8309 (m100) REVERT: D 582 ARG cc_start: 0.7134 (mmm160) cc_final: 0.6820 (tpt170) REVERT: F 403 ARG cc_start: 0.7788 (ptt180) cc_final: 0.7447 (ptm-80) REVERT: F 434 ILE cc_start: 0.7784 (mt) cc_final: 0.7540 (mt) REVERT: F 474 GLN cc_start: 0.7773 (tt0) cc_final: 0.7265 (tm-30) REVERT: F 486 PHE cc_start: 0.6447 (t80) cc_final: 0.6159 (t80) REVERT: F 487 ASN cc_start: 0.7712 (m-40) cc_final: 0.7107 (m-40) outliers start: 4 outliers final: 0 residues processed: 194 average time/residue: 0.1289 time to fit residues: 36.4984 Evaluate side-chains 131 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 42 GLN B 154 ASN B 239 HIS B 330 ASN B 345 HIS B 380 GLN B 429 GLN B 437 ASN B 442 GLN B 524 GLN B 586 ASN B 599 ASN B 601 ASN E 360 ASN E 370 ASN E 487 ASN E 493 GLN E 501 ASN D 102 GLN D 154 ASN D 239 HIS D 330 ASN D 374 HIS D 380 GLN D 429 GLN D 437 ASN D 442 GLN D 524 GLN D 586 ASN D 599 ASN D 601 ASN F 370 ASN F 487 ASN F 493 GLN F 501 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102429 restraints weight = 23227.695| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.42 r_work: 0.3029 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14946 Z= 0.122 Angle : 0.534 8.582 20292 Z= 0.281 Chirality : 0.042 0.159 2124 Planarity : 0.004 0.036 2632 Dihedral : 4.508 24.897 1952 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.58 % Allowed : 16.48 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.19), residues: 1780 helix: -0.24 (0.19), residues: 814 sheet: -1.40 (0.61), residues: 80 loop : -3.06 (0.17), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 403 TYR 0.013 0.001 TYR D 183 PHE 0.022 0.001 PHE E 486 TRP 0.007 0.001 TRP B 594 HIS 0.009 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00271 (14934) covalent geometry : angle 0.53179 (20268) SS BOND : bond 0.00666 ( 12) SS BOND : angle 1.56766 ( 24) hydrogen bonds : bond 0.05265 ( 558) hydrogen bonds : angle 4.16062 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.572 Fit side-chains REVERT: B 35 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7824 (mt-10) REVERT: B 51 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8194 (m110) REVERT: B 582 ARG cc_start: 0.7392 (mmm160) cc_final: 0.6968 (tpt170) REVERT: E 474 GLN cc_start: 0.7543 (tt0) cc_final: 0.7295 (tm-30) REVERT: D 35 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7713 (mt-10) REVERT: D 582 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6865 (tpt170) REVERT: F 464 PHE cc_start: 0.6938 (m-80) cc_final: 0.6468 (m-80) REVERT: F 474 GLN cc_start: 0.7734 (tt0) cc_final: 0.7328 (tm-30) outliers start: 25 outliers final: 10 residues processed: 163 average time/residue: 0.1192 time to fit residues: 29.7208 Evaluate side-chains 126 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 152 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103447 restraints weight = 23334.609| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.49 r_work: 0.3037 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14946 Z= 0.106 Angle : 0.510 8.031 20292 Z= 0.263 Chirality : 0.041 0.162 2124 Planarity : 0.004 0.034 2632 Dihedral : 4.165 23.036 1952 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.90 % Allowed : 17.05 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.19), residues: 1780 helix: 0.28 (0.19), residues: 804 sheet: -1.13 (0.63), residues: 80 loop : -2.66 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 716 TYR 0.010 0.001 TYR D 50 PHE 0.011 0.001 PHE E 400 TRP 0.007 0.001 TRP F 436 HIS 0.016 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00238 (14934) covalent geometry : angle 0.50650 (20268) SS BOND : bond 0.00566 ( 12) SS BOND : angle 1.77718 ( 24) hydrogen bonds : bond 0.04746 ( 558) hydrogen bonds : angle 3.94053 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.589 Fit side-chains REVERT: B 35 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7892 (mt-10) REVERT: B 51 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8047 (m110) REVERT: B 582 ARG cc_start: 0.7311 (mmm160) cc_final: 0.6790 (tpt170) REVERT: E 474 GLN cc_start: 0.7614 (tt0) cc_final: 0.7334 (tm-30) REVERT: E 487 ASN cc_start: 0.7376 (m110) cc_final: 0.6663 (m-40) REVERT: D 35 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7722 (mt-10) REVERT: D 719 ASP cc_start: 0.8062 (t0) cc_final: 0.7774 (t0) REVERT: F 464 PHE cc_start: 0.6907 (m-80) cc_final: 0.6465 (m-80) REVERT: F 474 GLN cc_start: 0.7691 (tt0) cc_final: 0.7324 (tm-30) outliers start: 30 outliers final: 13 residues processed: 151 average time/residue: 0.1043 time to fit residues: 24.8994 Evaluate side-chains 133 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 64 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 147 optimal weight: 0.0040 chunk 107 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 120 optimal weight: 0.0570 chunk 106 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 HIS B 653 GLN B 661 GLN D 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104774 restraints weight = 23212.476| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.42 r_work: 0.3066 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14946 Z= 0.097 Angle : 0.482 8.093 20292 Z= 0.247 Chirality : 0.040 0.158 2124 Planarity : 0.003 0.035 2632 Dihedral : 3.878 20.563 1952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.96 % Allowed : 17.81 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.20), residues: 1780 helix: 0.55 (0.19), residues: 816 sheet: -0.85 (0.64), residues: 80 loop : -2.48 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 219 TYR 0.009 0.001 TYR B 50 PHE 0.011 0.001 PHE E 400 TRP 0.007 0.001 TRP F 436 HIS 0.006 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00216 (14934) covalent geometry : angle 0.47921 (20268) SS BOND : bond 0.00577 ( 12) SS BOND : angle 1.50325 ( 24) hydrogen bonds : bond 0.04179 ( 558) hydrogen bonds : angle 3.79046 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.579 Fit side-chains REVERT: B 35 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7832 (mt-10) REVERT: E 409 GLN cc_start: 0.7504 (mt0) cc_final: 0.7292 (pt0) REVERT: E 474 GLN cc_start: 0.7643 (tt0) cc_final: 0.7389 (tm-30) REVERT: E 487 ASN cc_start: 0.7571 (m110) cc_final: 0.7195 (m110) REVERT: D 35 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7761 (mt-10) REVERT: D 582 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.7164 (mmt90) REVERT: D 719 ASP cc_start: 0.8000 (t0) cc_final: 0.7751 (t0) REVERT: F 474 GLN cc_start: 0.7678 (tt0) cc_final: 0.7419 (tm-30) outliers start: 31 outliers final: 14 residues processed: 156 average time/residue: 0.1078 time to fit residues: 25.8546 Evaluate side-chains 137 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 HIS B 638 ASN B 661 GLN D 58 ASN D 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098329 restraints weight = 23290.864| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.52 r_work: 0.2967 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14946 Z= 0.190 Angle : 0.583 10.135 20292 Z= 0.305 Chirality : 0.044 0.153 2124 Planarity : 0.004 0.036 2632 Dihedral : 4.382 21.058 1952 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.90 % Allowed : 18.38 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.20), residues: 1780 helix: 0.42 (0.19), residues: 822 sheet: -0.76 (0.64), residues: 78 loop : -2.40 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 582 TYR 0.020 0.001 TYR D 183 PHE 0.017 0.001 PHE D 684 TRP 0.011 0.001 TRP B 168 HIS 0.013 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00462 (14934) covalent geometry : angle 0.57938 (20268) SS BOND : bond 0.00604 ( 12) SS BOND : angle 2.00241 ( 24) hydrogen bonds : bond 0.06859 ( 558) hydrogen bonds : angle 4.14670 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.692 Fit side-chains REVERT: B 35 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7710 (mt-10) REVERT: B 582 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.7072 (mmt90) REVERT: E 474 GLN cc_start: 0.7800 (tt0) cc_final: 0.7431 (tm-30) REVERT: D 35 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7688 (mt-10) REVERT: D 582 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.6849 (tpt170) REVERT: F 409 GLN cc_start: 0.7514 (mt0) cc_final: 0.7151 (pt0) REVERT: F 474 GLN cc_start: 0.7875 (tt0) cc_final: 0.7426 (tm-30) outliers start: 30 outliers final: 17 residues processed: 149 average time/residue: 0.1107 time to fit residues: 26.0143 Evaluate side-chains 132 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 168 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 345 HIS B 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100865 restraints weight = 23182.405| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.57 r_work: 0.2992 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14946 Z= 0.142 Angle : 0.540 9.176 20292 Z= 0.281 Chirality : 0.043 0.167 2124 Planarity : 0.004 0.035 2632 Dihedral : 4.251 21.019 1952 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.03 % Allowed : 18.25 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.20), residues: 1780 helix: 0.55 (0.19), residues: 822 sheet: -0.66 (0.64), residues: 78 loop : -2.30 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 460 TYR 0.015 0.001 TYR D 183 PHE 0.013 0.001 PHE D 684 TRP 0.008 0.001 TRP B 168 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00339 (14934) covalent geometry : angle 0.53610 (20268) SS BOND : bond 0.00656 ( 12) SS BOND : angle 1.84872 ( 24) hydrogen bonds : bond 0.05717 ( 558) hydrogen bonds : angle 4.00881 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.631 Fit side-chains REVERT: B 35 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7804 (mt-10) REVERT: B 166 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8422 (tm-30) REVERT: B 582 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.7134 (mmt90) REVERT: E 409 GLN cc_start: 0.7586 (mt0) cc_final: 0.7301 (pt0) REVERT: E 412 PRO cc_start: 0.6356 (Cg_endo) cc_final: 0.6016 (Cg_exo) REVERT: E 474 GLN cc_start: 0.7829 (tt0) cc_final: 0.7436 (tm-30) REVERT: D 35 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7740 (mt-10) REVERT: D 166 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: F 474 GLN cc_start: 0.7890 (tt0) cc_final: 0.7362 (tm-30) outliers start: 32 outliers final: 20 residues processed: 151 average time/residue: 0.1061 time to fit residues: 25.1909 Evaluate side-chains 141 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 84 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 47 optimal weight: 0.0010 chunk 133 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102163 restraints weight = 23071.667| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.77 r_work: 0.3002 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14946 Z= 0.123 Angle : 0.520 8.951 20292 Z= 0.269 Chirality : 0.042 0.174 2124 Planarity : 0.003 0.035 2632 Dihedral : 4.104 21.323 1952 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.34 % Allowed : 17.93 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.20), residues: 1780 helix: 0.73 (0.19), residues: 814 sheet: -0.54 (0.65), residues: 78 loop : -2.25 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 355 TYR 0.013 0.001 TYR D 183 PHE 0.012 0.001 PHE B 684 TRP 0.007 0.001 TRP B 168 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00289 (14934) covalent geometry : angle 0.51653 (20268) SS BOND : bond 0.00670 ( 12) SS BOND : angle 1.77737 ( 24) hydrogen bonds : bond 0.05112 ( 558) hydrogen bonds : angle 3.89401 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.580 Fit side-chains REVERT: B 35 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7823 (mt-10) REVERT: E 412 PRO cc_start: 0.6365 (Cg_endo) cc_final: 0.6027 (Cg_exo) REVERT: E 474 GLN cc_start: 0.7818 (tt0) cc_final: 0.7416 (tm-30) REVERT: D 35 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7781 (mt-10) REVERT: D 582 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7127 (mmt90) REVERT: F 380 TYR cc_start: 0.4374 (OUTLIER) cc_final: 0.2320 (m-80) REVERT: F 409 GLN cc_start: 0.7634 (mt0) cc_final: 0.7303 (pt0) REVERT: F 474 GLN cc_start: 0.7817 (tt0) cc_final: 0.7312 (tm-30) outliers start: 37 outliers final: 28 residues processed: 156 average time/residue: 0.1100 time to fit residues: 26.8925 Evaluate side-chains 151 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 487 ASN F 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101888 restraints weight = 23170.790| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.71 r_work: 0.2994 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14946 Z= 0.132 Angle : 0.532 8.670 20292 Z= 0.275 Chirality : 0.042 0.157 2124 Planarity : 0.003 0.034 2632 Dihedral : 4.124 20.441 1952 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.47 % Allowed : 18.00 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.20), residues: 1780 helix: 0.73 (0.19), residues: 820 sheet: -0.50 (0.65), residues: 78 loop : -2.14 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 716 TYR 0.014 0.001 TYR D 183 PHE 0.013 0.001 PHE B 684 TRP 0.008 0.001 TRP B 168 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00311 (14934) covalent geometry : angle 0.52857 (20268) SS BOND : bond 0.00697 ( 12) SS BOND : angle 1.71547 ( 24) hydrogen bonds : bond 0.05464 ( 558) hydrogen bonds : angle 3.92435 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.496 Fit side-chains REVERT: B 35 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7802 (mt-10) REVERT: B 582 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.7130 (mmt90) REVERT: E 409 GLN cc_start: 0.7589 (mt0) cc_final: 0.7287 (pt0) REVERT: E 474 GLN cc_start: 0.7806 (tt0) cc_final: 0.7381 (tm-30) REVERT: D 35 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7754 (mt-10) REVERT: D 582 ARG cc_start: 0.7543 (mmm-85) cc_final: 0.7121 (mmt90) REVERT: F 380 TYR cc_start: 0.4285 (OUTLIER) cc_final: 0.2208 (m-80) REVERT: F 474 GLN cc_start: 0.7782 (tt0) cc_final: 0.7357 (tm-30) outliers start: 39 outliers final: 28 residues processed: 158 average time/residue: 0.1095 time to fit residues: 27.3986 Evaluate side-chains 150 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 164 optimal weight: 0.0030 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 chunk 74 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 overall best weight: 0.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 GLN B 661 GLN D 472 GLN D 661 GLN F 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106718 restraints weight = 23215.608| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.64 r_work: 0.3082 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14946 Z= 0.090 Angle : 0.488 8.508 20292 Z= 0.249 Chirality : 0.040 0.155 2124 Planarity : 0.003 0.033 2632 Dihedral : 3.733 21.702 1952 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.39 % Allowed : 18.95 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1780 helix: 1.01 (0.20), residues: 816 sheet: -0.38 (0.66), residues: 78 loop : -2.08 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.008 0.001 TYR D 50 PHE 0.010 0.001 PHE E 400 TRP 0.008 0.001 TRP F 436 HIS 0.002 0.000 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00193 (14934) covalent geometry : angle 0.48514 (20268) SS BOND : bond 0.00693 ( 12) SS BOND : angle 1.48801 ( 24) hydrogen bonds : bond 0.03510 ( 558) hydrogen bonds : angle 3.67150 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.624 Fit side-chains REVERT: B 35 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7759 (mt-10) REVERT: E 412 PRO cc_start: 0.6396 (Cg_endo) cc_final: 0.6077 (Cg_exo) REVERT: E 474 GLN cc_start: 0.7745 (tt0) cc_final: 0.7338 (tm-30) REVERT: D 35 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7758 (mt-10) REVERT: F 380 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.3151 (m-80) REVERT: F 409 GLN cc_start: 0.7500 (mt0) cc_final: 0.7216 (pt0) REVERT: F 474 GLN cc_start: 0.7714 (tt0) cc_final: 0.7278 (tm-30) outliers start: 22 outliers final: 16 residues processed: 143 average time/residue: 0.1146 time to fit residues: 25.3490 Evaluate side-chains 136 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 0.7980 chunk 155 optimal weight: 0.1980 chunk 52 optimal weight: 0.4980 chunk 176 optimal weight: 0.0030 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107286 restraints weight = 23090.997| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.42 r_work: 0.3104 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14946 Z= 0.091 Angle : 0.488 8.193 20292 Z= 0.250 Chirality : 0.040 0.154 2124 Planarity : 0.003 0.033 2632 Dihedral : 3.584 21.132 1952 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.14 % Allowed : 19.33 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1780 helix: 1.28 (0.20), residues: 804 sheet: -0.24 (0.67), residues: 78 loop : -2.05 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 582 TYR 0.007 0.001 TYR D 50 PHE 0.010 0.001 PHE E 400 TRP 0.007 0.001 TRP F 436 HIS 0.002 0.000 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00201 (14934) covalent geometry : angle 0.48573 (20268) SS BOND : bond 0.00574 ( 12) SS BOND : angle 1.49107 ( 24) hydrogen bonds : bond 0.03511 ( 558) hydrogen bonds : angle 3.57154 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.562 Fit side-chains REVERT: B 35 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7713 (mt-10) REVERT: E 403 ARG cc_start: 0.7685 (ptm-80) cc_final: 0.7480 (ptm-80) REVERT: E 409 GLN cc_start: 0.7545 (mt0) cc_final: 0.7305 (pt0) REVERT: E 412 PRO cc_start: 0.6434 (Cg_endo) cc_final: 0.6119 (Cg_exo) REVERT: E 474 GLN cc_start: 0.7711 (tt0) cc_final: 0.7312 (tm-30) REVERT: D 35 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7695 (mt-10) REVERT: F 380 TYR cc_start: 0.3998 (OUTLIER) cc_final: 0.2905 (m-80) REVERT: F 474 GLN cc_start: 0.7692 (tt0) cc_final: 0.7252 (tm-30) outliers start: 18 outliers final: 15 residues processed: 143 average time/residue: 0.1162 time to fit residues: 25.4254 Evaluate side-chains 142 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 95 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105763 restraints weight = 23090.797| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.51 r_work: 0.3072 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14946 Z= 0.098 Angle : 0.496 8.267 20292 Z= 0.253 Chirality : 0.040 0.153 2124 Planarity : 0.003 0.033 2632 Dihedral : 3.623 20.669 1952 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.20 % Allowed : 18.82 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.20), residues: 1780 helix: 1.34 (0.20), residues: 804 sheet: -0.20 (0.67), residues: 78 loop : -1.99 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 582 TYR 0.008 0.001 TYR B 183 PHE 0.010 0.001 PHE E 400 TRP 0.007 0.001 TRP D 477 HIS 0.002 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00223 (14934) covalent geometry : angle 0.49319 (20268) SS BOND : bond 0.00572 ( 12) SS BOND : angle 1.48448 ( 24) hydrogen bonds : bond 0.03929 ( 558) hydrogen bonds : angle 3.60222 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4419.97 seconds wall clock time: 76 minutes 3.36 seconds (4563.36 seconds total)