Starting phenix.real_space_refine on Tue Mar 3 21:35:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3c_35149/03_2026/8i3c_35149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3c_35149/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i3c_35149/03_2026/8i3c_35149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3c_35149/03_2026/8i3c_35149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i3c_35149/03_2026/8i3c_35149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3c_35149/03_2026/8i3c_35149.map" } 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-5986/lib/python3.9/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: 2.07, per 1000 atoms: 0.24 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: 0.57 Conformation dependent library (CDL) restraints added in 317.8 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: 0.25 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: 1.23 Time building geometry restraints manager: 0.82 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 - 23.53: 4981 23.53 - 47.06: 260 47.06 - 70.59: 45 70.59 - 94.13: 14 94.13 - 117.66: 4 Dihedral angle restraints: 5304 sinusoidal: 2146 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 5301 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: 0.01 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.100 Find NCS groups from input model: 0.060 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 15.628 117.658 3276 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 covalent geometry : bond 0.00939 ( 8848) covalent geometry : angle 1.02255 (12000) hydrogen bonds : bond 0.32219 ( 373) hydrogen bonds : angle 11.19130 ( 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 : 0.298 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: 0.7013 time to fit residues: 123.3773 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 : 0.412 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3848 r_free = 0.3848 target = 0.165094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118598 restraints weight = 9390.318| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.98 r_work: 0.3168 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8848 Z= 0.122 Angle : 0.599 6.812 12000 Z= 0.307 Chirality : 0.040 0.160 1432 Planarity : 0.006 0.053 1460 Dihedral : 9.751 100.730 1346 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.73 % Allowed : 12.37 % Favored : 83.90 % 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: -3.85 (0.20), residues: 1084 helix: -2.42 (0.16), residues: 602 sheet: -1.01 (0.52), residues: 80 loop : -2.88 (0.26), residues: 402 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 203 TRP 0.011 0.001 TRP B 447 HIS 0.003 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8848) covalent geometry : angle 0.59948 (12000) hydrogen bonds : bond 0.03942 ( 373) hydrogen bonds : angle 4.69118 ( 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 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7051 (ptpp) cc_final: 0.6688 (mttt) REVERT: A 174 THR cc_start: 0.7751 (m) cc_final: 0.7407 (t) REVERT: A 232 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: B 174 THR cc_start: 0.7728 (m) cc_final: 0.7493 (t) REVERT: B 183 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7805 (mm-30) REVERT: B 626 GLU cc_start: 0.6938 (pt0) cc_final: 0.6160 (pm20) outliers start: 35 outliers final: 8 residues processed: 153 average time/residue: 0.5689 time to fit residues: 92.8547 Evaluate side-chains 133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 571 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.0020 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3808 r_free = 0.3808 target = 0.161522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114588 restraints weight = 9251.676| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.82 r_work: 0.3098 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8848 Z= 0.223 Angle : 0.655 7.844 12000 Z= 0.327 Chirality : 0.044 0.149 1432 Planarity : 0.005 0.044 1460 Dihedral : 8.021 66.786 1339 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.16 % Allowed : 13.75 % Favored : 82.09 % 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: -2.87 (0.23), residues: 1084 helix: -1.39 (0.19), residues: 638 sheet: -0.92 (0.52), residues: 80 loop : -2.88 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.030 0.002 TYR B 475 PHE 0.011 0.001 PHE B 203 TRP 0.012 0.002 TRP B 447 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 8848) covalent geometry : angle 0.65533 (12000) hydrogen bonds : bond 0.04646 ( 373) hydrogen bonds : angle 4.31926 ( 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 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.5859 (mtp85) REVERT: A 183 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7840 (mm-30) REVERT: A 232 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: A 310 MET cc_start: 0.7920 (mtp) cc_final: 0.7711 (mtp) REVERT: A 408 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 450 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 626 GLU cc_start: 0.6912 (pt0) cc_final: 0.6179 (pm20) REVERT: B 179 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8271 (tp) REVERT: B 183 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7903 (mm-30) REVERT: B 232 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: B 266 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: B 408 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 450 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8171 (tp) REVERT: B 565 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8346 (m-80) outliers start: 39 outliers final: 12 residues processed: 142 average time/residue: 0.5963 time to fit residues: 90.1542 Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 283 GLU 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 88 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 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 565 TYR 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: 1.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 106 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3854 r_free = 0.3854 target = 0.166116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119032 restraints weight = 9367.262| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.80 r_work: 0.3188 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8848 Z= 0.104 Angle : 0.543 6.087 12000 Z= 0.273 Chirality : 0.040 0.141 1432 Planarity : 0.004 0.038 1460 Dihedral : 6.380 59.200 1339 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.84 % Allowed : 14.82 % Favored : 81.34 % 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: -1.78 (0.25), residues: 1084 helix: -0.40 (0.21), residues: 620 sheet: -1.29 (0.47), residues: 90 loop : -2.37 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 180 TYR 0.025 0.001 TYR B 475 PHE 0.008 0.001 PHE A 499 TRP 0.009 0.001 TRP A 447 HIS 0.002 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8848) covalent geometry : angle 0.54313 (12000) hydrogen bonds : bond 0.03076 ( 373) hydrogen bonds : angle 3.79896 ( 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 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.324 Fit side-chains REVERT: A 141 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.5784 (mtp85) REVERT: A 232 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: A 283 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5841 (mp0) REVERT: A 626 GLU cc_start: 0.6745 (pt0) cc_final: 0.6088 (pm20) REVERT: B 141 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.5603 (mtp85) REVERT: B 179 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8258 (tp) REVERT: B 183 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: B 232 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 266 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8116 (mt0) outliers start: 36 outliers final: 12 residues processed: 151 average time/residue: 0.5614 time to fit residues: 90.5001 Evaluate side-chains 139 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 565 TYR 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 183 GLU 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 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: 0.0970 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 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 = 0.162387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115826 restraints weight = 9411.883| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.74 r_work: 0.3152 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2359 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= 0.205 Angle : 0.616 5.715 12000 Z= 0.308 Chirality : 0.044 0.142 1432 Planarity : 0.005 0.039 1460 Dihedral : 6.152 61.441 1338 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.16 % Allowed : 15.99 % Favored : 79.85 % 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: -1.82 (0.25), residues: 1084 helix: -0.47 (0.21), residues: 640 sheet: -1.19 (0.48), residues: 90 loop : -2.43 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 180 TYR 0.028 0.002 TYR B 475 PHE 0.011 0.001 PHE B 499 TRP 0.012 0.002 TRP B 447 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8848) covalent geometry : angle 0.61617 (12000) hydrogen bonds : bond 0.04198 ( 373) hydrogen bonds : angle 3.97808 ( 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 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.286 Fit side-chains REVERT: A 141 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5840 (mtp85) REVERT: A 183 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7869 (mm-30) REVERT: A 232 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: A 626 GLU cc_start: 0.6844 (pt0) cc_final: 0.6164 (pm20) REVERT: B 141 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.5732 (mtp85) REVERT: B 179 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8304 (tp) REVERT: B 183 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: B 266 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: B 302 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7544 (m) outliers start: 39 outliers final: 16 residues processed: 143 average time/residue: 0.5359 time to fit residues: 81.8655 Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 565 TYR 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 183 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 566 VAL Chi-restraints excluded: chain B residue 571 SER 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: 0.5980 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.163319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117104 restraints weight = 9325.967| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.72 r_work: 0.3159 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8848 Z= 0.169 Angle : 0.590 6.371 12000 Z= 0.296 Chirality : 0.042 0.140 1432 Planarity : 0.005 0.044 1460 Dihedral : 5.941 57.715 1338 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.37 % Allowed : 16.10 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.25), residues: 1084 helix: -0.11 (0.21), residues: 624 sheet: -1.06 (0.48), residues: 90 loop : -2.13 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 180 TYR 0.026 0.002 TYR A 475 PHE 0.011 0.001 PHE B 499 TRP 0.011 0.002 TRP B 447 HIS 0.002 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8848) covalent geometry : angle 0.58966 (12000) hydrogen bonds : bond 0.03785 ( 373) hydrogen bonds : angle 3.88436 ( 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 167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.351 Fit side-chains REVERT: A 141 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.5781 (mtp85) REVERT: A 183 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7844 (mm-30) REVERT: A 226 SER cc_start: 0.8367 (m) cc_final: 0.8111 (p) REVERT: A 232 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: A 626 GLU cc_start: 0.6718 (pt0) cc_final: 0.6118 (pm20) REVERT: B 141 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.5511 (mtp85) REVERT: B 179 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8011 (tp) REVERT: B 180 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6848 (mpp-170) REVERT: B 183 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: B 232 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: B 266 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: B 283 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6754 (mt-10) outliers start: 41 outliers final: 21 residues processed: 151 average time/residue: 0.5639 time to fit residues: 90.8153 Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 302 VAL 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 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 183 GLU 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 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: 1.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.161851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115646 restraints weight = 9388.757| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.72 r_work: 0.3141 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8848 Z= 0.216 Angle : 0.626 6.049 12000 Z= 0.313 Chirality : 0.044 0.146 1432 Planarity : 0.005 0.048 1460 Dihedral : 5.974 59.914 1338 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.41 % Allowed : 17.59 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.25), residues: 1084 helix: -0.18 (0.21), residues: 626 sheet: -0.63 (0.53), residues: 80 loop : -2.05 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 180 TYR 0.028 0.002 TYR A 475 PHE 0.012 0.001 PHE B 499 TRP 0.012 0.002 TRP B 447 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 8848) covalent geometry : angle 0.62640 (12000) hydrogen bonds : bond 0.04210 ( 373) hydrogen bonds : angle 4.00534 ( 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 156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.361 Fit side-chains REVERT: A 141 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5785 (mtp85) REVERT: A 180 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6881 (mpp-170) REVERT: A 183 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7893 (mm-30) REVERT: A 226 SER cc_start: 0.8480 (m) cc_final: 0.8229 (p) REVERT: A 232 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: A 626 GLU cc_start: 0.6657 (pt0) cc_final: 0.6134 (pm20) REVERT: B 141 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5655 (mtp85) REVERT: B 179 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8275 (tp) REVERT: B 183 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: B 226 SER cc_start: 0.8487 (m) cc_final: 0.8262 (p) REVERT: B 266 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: B 283 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6921 (mt-10) outliers start: 32 outliers final: 19 residues processed: 143 average time/residue: 0.5790 time to fit residues: 88.2367 Evaluate side-chains 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 302 VAL 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 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 183 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 566 VAL 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: 3.9990 chunk 85 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117471 restraints weight = 9292.753| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.67 r_work: 0.3108 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8848 Z= 0.171 Angle : 0.591 6.048 12000 Z= 0.296 Chirality : 0.042 0.140 1432 Planarity : 0.005 0.051 1460 Dihedral : 5.763 56.505 1338 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.30 % Allowed : 18.02 % 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: -1.15 (0.26), residues: 1084 helix: 0.02 (0.21), residues: 624 sheet: -0.81 (0.48), residues: 90 loop : -2.00 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 180 TYR 0.026 0.002 TYR A 475 PHE 0.012 0.001 PHE A 499 TRP 0.011 0.002 TRP B 447 HIS 0.002 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8848) covalent geometry : angle 0.59092 (12000) hydrogen bonds : bond 0.03800 ( 373) hydrogen bonds : angle 3.88907 ( 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 157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.314 Fit side-chains REVERT: A 85 SER cc_start: 0.7389 (p) cc_final: 0.7135 (t) REVERT: A 136 LYS cc_start: 0.7858 (mptt) cc_final: 0.7571 (tppt) REVERT: A 141 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5752 (mtp85) REVERT: A 180 ARG cc_start: 0.7218 (mtm110) cc_final: 0.6837 (mpp-170) REVERT: A 183 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7840 (mm-30) REVERT: A 193 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8502 (pttm) REVERT: A 226 SER cc_start: 0.8449 (m) cc_final: 0.8188 (p) REVERT: A 232 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: A 283 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6743 (mt-10) REVERT: A 626 GLU cc_start: 0.6690 (pt0) cc_final: 0.6140 (pm20) REVERT: B 136 LYS cc_start: 0.7879 (mptt) cc_final: 0.7596 (tppt) REVERT: B 141 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.5611 (mtp85) REVERT: B 179 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7975 (tp) REVERT: B 180 ARG cc_start: 0.7216 (mtm110) cc_final: 0.6849 (mpp-170) REVERT: B 183 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: B 193 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8519 (pttm) REVERT: B 226 SER cc_start: 0.8453 (m) cc_final: 0.8212 (p) REVERT: B 266 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: B 283 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6972 (mt-10) REVERT: B 626 GLU cc_start: 0.6712 (pt0) cc_final: 0.6134 (pm20) outliers start: 31 outliers final: 21 residues processed: 143 average time/residue: 0.5833 time to fit residues: 88.8190 Evaluate side-chains 151 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 302 VAL 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 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 183 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 300 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117195 restraints weight = 9366.485| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.76 r_work: 0.3153 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2584 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= 0.177 Angle : 0.599 6.740 12000 Z= 0.299 Chirality : 0.043 0.141 1432 Planarity : 0.005 0.047 1460 Dihedral : 5.836 56.986 1338 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.30 % Allowed : 18.34 % Favored : 78.36 % 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: -1.18 (0.26), residues: 1084 helix: 0.01 (0.21), residues: 632 sheet: -0.73 (0.48), residues: 90 loop : -2.13 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 180 TYR 0.027 0.002 TYR B 475 PHE 0.012 0.001 PHE B 499 TRP 0.011 0.002 TRP B 447 HIS 0.002 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8848) covalent geometry : angle 0.59925 (12000) hydrogen bonds : bond 0.03892 ( 373) hydrogen bonds : angle 3.90565 ( 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 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.324 Fit side-chains REVERT: A 85 SER cc_start: 0.7461 (p) cc_final: 0.7151 (t) REVERT: A 136 LYS cc_start: 0.7786 (mptt) cc_final: 0.7521 (tppt) REVERT: A 141 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.5804 (mtp85) REVERT: A 180 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6872 (mpp-170) REVERT: A 183 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: A 193 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8521 (pttm) REVERT: A 226 SER cc_start: 0.8472 (m) cc_final: 0.8229 (p) REVERT: A 232 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: A 283 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6929 (mt-10) REVERT: A 626 GLU cc_start: 0.6622 (pt0) cc_final: 0.6180 (pm20) REVERT: B 136 LYS cc_start: 0.7809 (mptt) cc_final: 0.7545 (tppt) REVERT: B 141 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5671 (mtp85) REVERT: B 179 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7955 (tp) REVERT: B 180 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6870 (mpp-170) REVERT: B 183 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: B 193 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8518 (pttm) REVERT: B 226 SER cc_start: 0.8468 (m) cc_final: 0.8251 (p) REVERT: B 232 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: B 266 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: B 283 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7091 (mt-10) REVERT: B 626 GLU cc_start: 0.6608 (pt0) cc_final: 0.6094 (pm20) outliers start: 31 outliers final: 21 residues processed: 145 average time/residue: 0.5954 time to fit residues: 91.8468 Evaluate side-chains 156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 183 GLU 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 300 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119360 restraints weight = 9295.492| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.67 r_work: 0.3193 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8848 Z= 0.127 Angle : 0.557 6.767 12000 Z= 0.278 Chirality : 0.041 0.133 1432 Planarity : 0.004 0.046 1460 Dihedral : 5.624 51.800 1338 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.99 % Allowed : 18.98 % 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: -0.73 (0.26), residues: 1084 helix: 0.45 (0.22), residues: 610 sheet: -0.60 (0.48), residues: 90 loop : -1.94 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 180 TYR 0.024 0.002 TYR A 475 PHE 0.011 0.001 PHE A 499 TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8848) covalent geometry : angle 0.55698 (12000) hydrogen bonds : bond 0.03357 ( 373) hydrogen bonds : angle 3.76187 ( 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 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.322 Fit side-chains REVERT: A 85 SER cc_start: 0.7373 (p) cc_final: 0.7088 (t) REVERT: A 141 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5886 (mtp85) REVERT: A 180 ARG cc_start: 0.7233 (mtm110) cc_final: 0.6855 (mpp-170) REVERT: A 183 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: A 193 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8496 (pttm) REVERT: A 226 SER cc_start: 0.8396 (m) cc_final: 0.8143 (p) REVERT: A 232 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: A 283 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6969 (mt-10) REVERT: B 141 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5576 (mtp85) REVERT: B 179 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7888 (tp) REVERT: B 180 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6843 (mpp-170) REVERT: B 183 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: B 193 LYS cc_start: 0.9110 (mtmm) cc_final: 0.8491 (pttm) REVERT: B 226 SER cc_start: 0.8392 (m) cc_final: 0.8140 (p) REVERT: B 283 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7036 (mt-10) REVERT: B 626 GLU cc_start: 0.6479 (pt0) cc_final: 0.6015 (pm20) outliers start: 28 outliers final: 20 residues processed: 139 average time/residue: 0.5490 time to fit residues: 81.5507 Evaluate side-chains 149 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 183 GLU 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 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 94 optimal weight: 0.0030 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3831 r_free = 0.3831 target = 0.164098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118149 restraints weight = 9245.124| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.68 r_work: 0.3144 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8848 Z= 0.146 Angle : 0.570 6.568 12000 Z= 0.284 Chirality : 0.041 0.135 1432 Planarity : 0.004 0.043 1460 Dihedral : 5.613 52.334 1338 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.99 % Allowed : 19.62 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.26), residues: 1084 helix: 0.47 (0.22), residues: 614 sheet: -0.49 (0.49), residues: 90 loop : -1.82 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 180 TYR 0.025 0.002 TYR A 475 PHE 0.012 0.001 PHE A 499 TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8848) covalent geometry : angle 0.57043 (12000) hydrogen bonds : bond 0.03587 ( 373) hydrogen bonds : angle 3.78720 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.21 seconds wall clock time: 59 minutes 5.74 seconds (3545.74 seconds total)