Starting phenix.real_space_refine on Thu Jul 2 13:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.cif" model { file = "/net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3c_35149/07_2026/8i3c_35149.cif" } resolution = 2.85 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= 0.003 sd= 0.090 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 58 5.16 5 C 5660 2.51 5 N 1440 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 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: 8664 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4297 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 533} Chain breaks: 4 Chain: "B" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4297 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 533} Chain breaks: 4 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.43, per 1000 atoms: 0.17 Number of scatterers: 8664 At special positions: 0 Unit cell: (80.51, 100.43, 124.5, 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 58 16.00 O 1506 8.00 N 1440 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 372.1 milliseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 59.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.621A pdb=" N LYS A 140 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.891A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.534A pdb=" N CYS A 194 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 195 " --> pdb=" O THR A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 195' Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.522A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.925A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.575A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.601A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.535A pdb=" N ALA A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.057A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.951A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.615A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.517A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.534A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.605A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.874A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.896A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.829A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.058A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.532A pdb=" N LEU A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.619A pdb=" N GLU A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 623 through 628' Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 643 through 660 removed outlier: 3.675A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 137 through 140 removed outlier: 3.621A pdb=" N LYS B 140 " --> pdb=" O GLN B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.892A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.534A pdb=" N CYS B 194 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.524A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.925A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.575A pdb=" N PHE B 275 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.600A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.537A pdb=" N ALA B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.057A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.952A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 404' Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.615A pdb=" N PHE B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.517A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.534A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 477 through 492 removed outlier: 3.605A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 486 " --> pdb=" O MET B 482 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.874A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.896A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.828A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.058A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 605 removed outlier: 3.531A pdb=" N LEU B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.619A pdb=" N GLU B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 628 " --> pdb=" O PHE B 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 623 through 628' Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 643 through 660 removed outlier: 3.675A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 653 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.260A pdb=" N ILE A 83 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ARG A 48 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 85 " --> pdb=" O CYS A 46 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS A 46 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.360A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 277 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 91 removed outlier: 6.260A pdb=" N ILE B 83 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG B 48 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 85 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS B 46 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE B 42 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 128 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP B 44 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS B 126 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.359A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 277 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 290 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1314 1.29 - 1.42: 2294 1.42 - 1.55: 5136 1.55 - 1.68: 12 1.68 - 1.81: 92 Bond restraints: 8848 Sorted by residual: bond pdb=" C PHE A 441 " pdb=" O PHE A 441 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.28e-02 6.10e+03 4.00e+01 bond pdb=" C PHE B 441 " pdb=" O PHE B 441 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.34e-02 5.57e+03 3.64e+01 bond pdb=" C ILE A 445 " pdb=" O ILE A 445 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.23e-02 6.61e+03 2.48e+01 bond pdb=" C ILE B 445 " pdb=" O ILE B 445 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.23e-02 6.61e+03 2.37e+01 bond pdb=" C GLY B 438 " pdb=" O GLY B 438 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.35e-02 5.49e+03 2.18e+01 ... (remaining 8843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 11157 1.77 - 3.55: 660 3.55 - 5.32: 130 5.32 - 7.09: 41 7.09 - 8.87: 12 Bond angle restraints: 12000 Sorted by residual: angle pdb=" N VAL B 641 " pdb=" CA VAL B 641 " pdb=" C VAL B 641 " ideal model delta sigma weight residual 112.96 106.90 6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N VAL A 641 " pdb=" CA VAL A 641 " pdb=" C VAL A 641 " ideal model delta sigma weight residual 112.96 106.93 6.03 1.00e+00 1.00e+00 3.64e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 112.96 107.88 5.08 1.00e+00 1.00e+00 2.58e+01 angle pdb=" N VAL B 414 " pdb=" CA VAL B 414 " pdb=" C VAL B 414 " ideal model delta sigma weight residual 112.96 107.90 5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" N ASP B 435 " pdb=" CA ASP B 435 " pdb=" C ASP B 435 " ideal model delta sigma weight residual 113.50 107.59 5.91 1.23e+00 6.61e-01 2.31e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4672 17.79 - 35.58: 411 35.58 - 53.36: 66 53.36 - 71.15: 29 71.15 - 88.94: 10 Dihedral angle restraints: 5188 sinusoidal: 2030 harmonic: 3158 Sorted by residual: dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LYS A 661 " pdb=" CA LYS A 661 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LYS B 661 " pdb=" CA LYS B 661 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LYS B 285 " pdb=" C LYS B 285 " pdb=" N CYS B 286 " pdb=" CA CYS B 286 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1037 0.057 - 0.113: 325 0.113 - 0.170: 54 0.170 - 0.226: 9 0.226 - 0.283: 7 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CB VAL B 566 " pdb=" CA VAL B 566 " pdb=" CG1 VAL B 566 " pdb=" CG2 VAL B 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB VAL B 559 " pdb=" CA VAL B 559 " pdb=" CG1 VAL B 559 " pdb=" CG2 VAL B 559 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1429 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 661 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS B 661 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 661 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS B 662 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 661 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS A 661 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS A 661 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS A 662 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 350 " -0.049 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO B 351 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 351 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 351 " -0.042 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2793 2.83 - 3.35: 7222 3.35 - 3.87: 13519 3.87 - 4.38: 16632 4.38 - 4.90: 29168 Nonbonded interactions: 69334 Sorted by model distance: nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.313 3.040 nonbonded pdb=" NH2 ARG A 470 " pdb=" O LYS A 661 " model vdw 2.314 3.120 nonbonded pdb=" O SER B 472 " pdb=" OG SER B 472 " model vdw 2.314 3.040 nonbonded pdb=" NH2 ARG B 470 " pdb=" O LYS B 661 " model vdw 2.314 3.120 nonbonded pdb=" OE1 GLU A 462 " pdb=" OH TYR A 480 " model vdw 2.320 3.040 ... (remaining 69329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.030 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.790 Find NCS groups from input model: 0.070 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.009 0.081 8848 Z= 0.443 Angle : 1.023 8.868 12000 Z= 0.581 Chirality : 0.058 0.283 1432 Planarity : 0.008 0.075 1460 Dihedral : 14.756 88.940 3160 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.81 % Allowed : 6.50 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.17 (0.16), residues: 1084 helix: -4.71 (0.07), residues: 600 sheet: -1.01 (0.57), residues: 80 loop : -3.41 (0.24), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.035 0.003 TYR A 475 PHE 0.020 0.002 PHE A 499 TRP 0.018 0.003 TRP B 425 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00939 / 0.44 ( 8848) covalent geometry : angle 1.02255 / 0.58 (12000) hydrogen bonds : bond 0.32219 / 21.58 ( 373) hydrogen bonds : angle 11.19130 / 7.90 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.205 Fit side-chains REVERT: A 491 MET cc_start: 0.8585 (mmp) cc_final: 0.8367 (mmt) REVERT: B 491 MET cc_start: 0.8600 (mmp) cc_final: 0.8392 (mmp) outliers start: 17 outliers final: 4 residues processed: 167 average time/residue: 0.4995 time to fit residues: 88.1335 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 531 GLN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119176 restraints weight = 9364.340| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.89 r_work: 0.3130 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8848 Z= 0.125 Angle : 0.591 5.388 12000 Z= 0.308 Chirality : 0.040 0.164 1432 Planarity : 0.006 0.053 1460 Dihedral : 8.112 104.117 1230 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.73 % Allowed : 12.47 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.02 (0.20), residues: 1084 helix: -2.46 (0.16), residues: 618 sheet: -1.00 (0.53), residues: 80 loop : -3.15 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.027 0.001 TYR A 475 PHE 0.007 0.001 PHE A 499 TRP 0.011 0.001 TRP A 447 HIS 0.003 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8848) covalent geometry : angle 0.59123 / 0.31 (12000) hydrogen bonds : bond 0.04054 / 2.67 ( 373) hydrogen bonds : angle 4.69612 / 3.24 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 174 THR cc_start: 0.7786 (m) cc_final: 0.7435 (t) REVERT: A 232 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: A 450 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8227 (tp) REVERT: A 626 GLU cc_start: 0.6905 (pt0) cc_final: 0.6176 (pm20) REVERT: B 174 THR cc_start: 0.7797 (m) cc_final: 0.7563 (t) REVERT: B 450 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8180 (tp) REVERT: B 626 GLU cc_start: 0.6944 (pt0) cc_final: 0.6160 (pm20) outliers start: 35 outliers final: 9 residues processed: 151 average time/residue: 0.4348 time to fit residues: 70.3839 Evaluate side-chains 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS A 266 GLN B 154 HIS B 461 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107876 restraints weight = 9272.414| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.87 r_work: 0.3101 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8848 Z= 0.246 Angle : 0.652 5.897 12000 Z= 0.331 Chirality : 0.045 0.150 1432 Planarity : 0.006 0.047 1460 Dihedral : 7.357 71.401 1224 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.37 % Allowed : 13.33 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.23), residues: 1084 helix: -1.45 (0.19), residues: 638 sheet: -0.88 (0.52), residues: 80 loop : -2.91 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 180 TYR 0.031 0.002 TYR B 475 PHE 0.011 0.002 PHE B 203 TRP 0.013 0.002 TRP B 447 HIS 0.003 0.001 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.25 ( 8848) covalent geometry : angle 0.65230 / 0.33 (12000) hydrogen bonds : bond 0.04784 / 3.13 ( 373) hydrogen bonds : angle 4.38996 / 3.01 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.205 Fit side-chains REVERT: A 140 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7868 (tppt) REVERT: A 141 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5772 (mtp85) REVERT: A 183 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7867 (mm-30) REVERT: A 226 SER cc_start: 0.8340 (m) cc_final: 0.8076 (p) REVERT: A 232 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: A 408 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 450 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8164 (tp) REVERT: A 626 GLU cc_start: 0.6932 (pt0) cc_final: 0.6175 (pm20) REVERT: B 179 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8244 (tp) REVERT: B 226 SER cc_start: 0.8354 (m) cc_final: 0.8033 (p) REVERT: B 232 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: B 266 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: B 408 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 450 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8141 (tp) outliers start: 41 outliers final: 14 residues processed: 143 average time/residue: 0.4703 time to fit residues: 71.7966 Evaluate side-chains 144 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 662 HIS B 461 GLN B 662 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117055 restraints weight = 9360.185| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.83 r_work: 0.3105 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8848 Z= 0.138 Angle : 0.565 5.636 12000 Z= 0.286 Chirality : 0.041 0.156 1432 Planarity : 0.005 0.039 1460 Dihedral : 6.850 69.615 1224 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.62 % Allowed : 15.35 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.24), residues: 1084 helix: -0.59 (0.21), residues: 622 sheet: -1.26 (0.48), residues: 90 loop : -2.43 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 180 TYR 0.026 0.002 TYR A 475 PHE 0.010 0.001 PHE A 499 TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8848) covalent geometry : angle 0.56542 / 0.29 (12000) hydrogen bonds : bond 0.03558 / 2.33 ( 373) hydrogen bonds : angle 3.96786 / 2.70 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.190 Fit side-chains REVERT: A 141 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5810 (mtp85) REVERT: A 183 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7854 (mm-30) REVERT: A 232 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: A 266 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8116 (mt0) REVERT: A 450 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8178 (tp) REVERT: A 626 GLU cc_start: 0.6775 (pt0) cc_final: 0.6080 (pm20) REVERT: B 141 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.5498 (mtp85) REVERT: B 179 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8285 (tp) REVERT: B 232 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: B 266 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: B 286 CYS cc_start: 0.7198 (t) cc_final: 0.6929 (t) REVERT: B 450 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8162 (tp) outliers start: 34 outliers final: 13 residues processed: 148 average time/residue: 0.4201 time to fit residues: 66.5960 Evaluate side-chains 145 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN B 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.162168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114937 restraints weight = 9358.059| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.83 r_work: 0.3109 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8848 Z= 0.198 Angle : 0.610 5.717 12000 Z= 0.307 Chirality : 0.044 0.155 1432 Planarity : 0.005 0.045 1460 Dihedral : 6.860 70.207 1222 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.26 % Allowed : 15.35 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.25), residues: 1084 helix: -0.53 (0.21), residues: 640 sheet: -1.18 (0.49), residues: 90 loop : -2.47 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 180 TYR 0.028 0.002 TYR A 475 PHE 0.012 0.001 PHE B 499 TRP 0.011 0.002 TRP B 447 HIS 0.003 0.001 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 ( 8848) covalent geometry : angle 0.61001 / 0.31 (12000) hydrogen bonds : bond 0.04131 / 2.69 ( 373) hydrogen bonds : angle 4.01332 / 2.73 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.304 Fit side-chains REVERT: A 141 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5693 (mtp85) REVERT: A 183 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7842 (mm-30) REVERT: A 226 SER cc_start: 0.8365 (m) cc_final: 0.8095 (p) REVERT: A 232 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: A 266 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: A 450 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8143 (tp) REVERT: A 626 GLU cc_start: 0.6850 (pt0) cc_final: 0.6172 (pm20) REVERT: B 141 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.5411 (mtp85) REVERT: B 179 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8294 (tp) REVERT: B 232 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: B 266 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: B 302 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7514 (m) REVERT: B 450 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8134 (tp) outliers start: 40 outliers final: 19 residues processed: 145 average time/residue: 0.4550 time to fit residues: 70.6192 Evaluate side-chains 149 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 83 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.163322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111875 restraints weight = 9316.579| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.79 r_work: 0.3113 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8848 Z= 0.169 Angle : 0.589 5.934 12000 Z= 0.295 Chirality : 0.043 0.160 1432 Planarity : 0.005 0.045 1460 Dihedral : 6.661 69.847 1222 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.58 % Allowed : 15.78 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.25), residues: 1084 helix: -0.29 (0.21), residues: 644 sheet: -1.05 (0.49), residues: 90 loop : -2.32 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 180 TYR 0.027 0.002 TYR B 475 PHE 0.012 0.001 PHE B 499 TRP 0.011 0.002 TRP A 447 HIS 0.002 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 8848) covalent geometry : angle 0.58878 / 0.30 (12000) hydrogen bonds : bond 0.03782 / 2.47 ( 373) hydrogen bonds : angle 3.91714 / 2.66 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.301 Fit side-chains REVERT: A 141 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5718 (mtp85) REVERT: A 183 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7798 (mm-30) REVERT: A 226 SER cc_start: 0.8349 (m) cc_final: 0.8083 (p) REVERT: A 232 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: A 266 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: A 283 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6767 (mt-10) REVERT: A 450 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8152 (tp) REVERT: A 626 GLU cc_start: 0.6728 (pt0) cc_final: 0.6100 (pm20) REVERT: B 141 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5372 (mtp85) REVERT: B 179 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7981 (tp) REVERT: B 180 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6792 (mpp-170) REVERT: B 226 SER cc_start: 0.8340 (m) cc_final: 0.8067 (p) REVERT: B 232 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: B 266 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: B 286 CYS cc_start: 0.7306 (t) cc_final: 0.7030 (t) REVERT: B 302 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7485 (m) REVERT: B 450 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8139 (tp) outliers start: 43 outliers final: 21 residues processed: 154 average time/residue: 0.4394 time to fit residues: 72.4567 Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118552 restraints weight = 9350.015| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.66 r_work: 0.3130 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8848 Z= 0.141 Angle : 0.569 5.895 12000 Z= 0.284 Chirality : 0.041 0.165 1432 Planarity : 0.004 0.049 1460 Dihedral : 6.465 69.687 1222 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.05 % Allowed : 17.06 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.26), residues: 1084 helix: 0.08 (0.22), residues: 626 sheet: -0.89 (0.48), residues: 90 loop : -2.09 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 180 TYR 0.025 0.002 TYR A 475 PHE 0.011 0.001 PHE B 499 TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 8848) covalent geometry : angle 0.56925 / 0.28 (12000) hydrogen bonds : bond 0.03485 / 2.27 ( 373) hydrogen bonds : angle 3.80178 / 2.58 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.328 Fit side-chains REVERT: A 141 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.5794 (mtp85) REVERT: A 180 ARG cc_start: 0.7215 (mtm110) cc_final: 0.6852 (mpp-170) REVERT: A 183 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: A 193 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8490 (pttm) REVERT: A 226 SER cc_start: 0.8356 (m) cc_final: 0.8097 (p) REVERT: A 232 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: A 283 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6852 (mt-10) REVERT: A 450 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8153 (tp) REVERT: A 568 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7973 (mttm) REVERT: B 141 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.5453 (mtp85) REVERT: B 179 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7935 (tp) REVERT: B 180 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6801 (mpp-170) REVERT: B 226 SER cc_start: 0.8353 (m) cc_final: 0.8093 (p) REVERT: B 232 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: B 266 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: B 286 CYS cc_start: 0.7396 (t) cc_final: 0.7157 (t) REVERT: B 450 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8147 (tp) outliers start: 38 outliers final: 22 residues processed: 150 average time/residue: 0.4509 time to fit residues: 72.5163 Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 5.9990 chunk 85 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.165898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119330 restraints weight = 9316.616| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.75 r_work: 0.3179 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 0.026 8848 Z= 0.113 Angle : 0.537 5.656 12000 Z= 0.268 Chirality : 0.040 0.140 1432 Planarity : 0.004 0.041 1460 Dihedral : 6.189 69.578 1222 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.20 % Allowed : 18.02 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.26), residues: 1084 helix: 0.51 (0.22), residues: 610 sheet: -0.74 (0.48), residues: 90 loop : -2.03 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 180 TYR 0.023 0.001 TYR B 475 PHE 0.011 0.001 PHE B 499 TRP 0.009 0.001 TRP A 447 HIS 0.001 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 8848) covalent geometry : angle 0.53717 / 0.27 (12000) hydrogen bonds : bond 0.03088 / 2.04 ( 373) hydrogen bonds : angle 3.68306 / 2.49 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.266 Fit side-chains REVERT: A 136 LYS cc_start: 0.7796 (mptt) cc_final: 0.7544 (tppt) REVERT: A 183 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7908 (mm-30) REVERT: A 193 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8484 (pttm) REVERT: A 226 SER cc_start: 0.8390 (m) cc_final: 0.8111 (p) REVERT: A 232 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: A 283 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7020 (mt-10) REVERT: A 286 CYS cc_start: 0.7431 (t) cc_final: 0.7228 (t) REVERT: A 450 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8241 (tp) REVERT: B 136 LYS cc_start: 0.7799 (mptt) cc_final: 0.7543 (tppt) REVERT: B 141 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5588 (mtp85) REVERT: B 179 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8252 (tp) REVERT: B 193 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8486 (pttm) REVERT: B 226 SER cc_start: 0.8391 (m) cc_final: 0.8156 (p) REVERT: B 232 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: B 266 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: B 450 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8232 (tp) REVERT: B 626 GLU cc_start: 0.6644 (pt0) cc_final: 0.6156 (pm20) outliers start: 30 outliers final: 17 residues processed: 144 average time/residue: 0.4362 time to fit residues: 67.6546 Evaluate side-chains 148 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.0970 chunk 71 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.0040 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123700 restraints weight = 9342.184| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.68 r_work: 0.3226 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8848 Z= 0.095 Angle : 0.528 5.953 12000 Z= 0.262 Chirality : 0.039 0.127 1432 Planarity : 0.004 0.055 1460 Dihedral : 5.948 69.405 1222 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.99 % Allowed : 18.34 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.26), residues: 1084 helix: 0.78 (0.22), residues: 612 sheet: -0.59 (0.48), residues: 90 loop : -1.85 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 180 TYR 0.021 0.001 TYR A 475 PHE 0.010 0.001 PHE B 499 TRP 0.009 0.001 TRP A 447 HIS 0.001 0.000 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 8848) covalent geometry : angle 0.52770 / 0.26 (12000) hydrogen bonds : bond 0.02803 / 1.85 ( 373) hydrogen bonds : angle 3.56238 / 2.42 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.278 Fit side-chains REVERT: A 85 SER cc_start: 0.7364 (p) cc_final: 0.7047 (t) REVERT: A 183 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: A 193 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8491 (pttm) REVERT: A 226 SER cc_start: 0.8365 (m) cc_final: 0.8090 (p) REVERT: A 283 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7046 (mt-10) REVERT: A 450 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8244 (tp) REVERT: B 141 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.5569 (mtp85) REVERT: B 179 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8220 (tp) REVERT: B 193 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8471 (pttm) REVERT: B 226 SER cc_start: 0.8365 (m) cc_final: 0.8132 (p) REVERT: B 232 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: B 450 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8238 (tp) REVERT: B 626 GLU cc_start: 0.6406 (pt0) cc_final: 0.5947 (pm20) outliers start: 28 outliers final: 15 residues processed: 149 average time/residue: 0.4215 time to fit residues: 67.6509 Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 7 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.163688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112283 restraints weight = 9253.755| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.79 r_work: 0.3113 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8848 Z= 0.172 Angle : 0.589 6.382 12000 Z= 0.292 Chirality : 0.043 0.139 1432 Planarity : 0.005 0.059 1460 Dihedral : 6.240 70.030 1222 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.67 % Allowed : 19.30 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.26), residues: 1084 helix: 0.61 (0.22), residues: 612 sheet: -0.45 (0.48), residues: 90 loop : -1.76 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 180 TYR 0.025 0.002 TYR B 475 PHE 0.011 0.001 PHE B 499 TRP 0.010 0.001 TRP B 447 HIS 0.002 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 ( 8848) covalent geometry : angle 0.58906 / 0.29 (12000) hydrogen bonds : bond 0.03795 / 2.47 ( 373) hydrogen bonds : angle 3.78521 / 2.57 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.220 Fit side-chains REVERT: A 85 SER cc_start: 0.7306 (p) cc_final: 0.7034 (t) REVERT: A 183 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: A 193 LYS cc_start: 0.9110 (mtmm) cc_final: 0.8471 (pttm) REVERT: A 226 SER cc_start: 0.8410 (m) cc_final: 0.8082 (p) REVERT: A 283 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6969 (mt-10) REVERT: A 296 MET cc_start: 0.7964 (mmm) cc_final: 0.7746 (mmm) REVERT: A 450 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 141 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.5549 (mtp85) REVERT: B 179 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7921 (tp) REVERT: B 180 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6806 (mpp-170) REVERT: B 193 LYS cc_start: 0.9108 (mtmm) cc_final: 0.8462 (pttm) REVERT: B 226 SER cc_start: 0.8408 (m) cc_final: 0.8171 (p) REVERT: B 450 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8157 (tp) REVERT: B 626 GLU cc_start: 0.6542 (pt0) cc_final: 0.6037 (pm20) outliers start: 25 outliers final: 13 residues processed: 135 average time/residue: 0.4175 time to fit residues: 60.7512 Evaluate side-chains 134 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.165061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119257 restraints weight = 9226.714| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.70 r_work: 0.3192 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8848 Z= 0.134 Angle : 0.561 6.264 12000 Z= 0.278 Chirality : 0.041 0.130 1432 Planarity : 0.005 0.059 1460 Dihedral : 6.220 69.101 1222 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.56 % Allowed : 19.51 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1084 helix: 0.71 (0.22), residues: 612 sheet: -0.35 (0.48), residues: 90 loop : -1.73 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 180 TYR 0.024 0.002 TYR B 475 PHE 0.011 0.001 PHE B 499 TRP 0.009 0.001 TRP A 447 HIS 0.002 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 8848) covalent geometry : angle 0.56107 / 0.28 (12000) hydrogen bonds : bond 0.03364 / 2.19 ( 373) hydrogen bonds : angle 3.70092 / 2.51 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.07 seconds wall clock time: 48 minutes 14.24 seconds (2894.24 seconds total)