Starting phenix.real_space_refine on Wed Mar 4 18:11:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nmn_12466/03_2026/7nmn_12466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nmn_12466/03_2026/7nmn_12466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nmn_12466/03_2026/7nmn_12466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nmn_12466/03_2026/7nmn_12466.map" model { file = "/net/cci-nas-00/data/ceres_data/7nmn_12466/03_2026/7nmn_12466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nmn_12466/03_2026/7nmn_12466.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 128 5.16 5 C 10000 2.51 5 N 2608 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s 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: 15436 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3859 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 16, 'TRANS': 452} Chain breaks: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 3.21, per 1000 atoms: 0.21 Number of scatterers: 15436 At special positions: 0 Unit cell: (128.905, 128.905, 120.015, 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 128 16.00 O 2700 8.00 N 2608 7.00 C 10000 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: 1.27 Conformation dependent library (CDL) restraints added in 554.1 milliseconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 69.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.069A pdb=" N GLY A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 287 removed outlier: 3.575A pdb=" N PHE A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 4.066A pdb=" N THR A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.656A pdb=" N ILE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.696A pdb=" N LEU A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 444 Proline residue: A 441 - end of helix removed outlier: 3.658A pdb=" N GLN A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.571A pdb=" N TYR A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 542 " --> pdb=" O TYR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 558 Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.581A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS A 589 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A 590 " --> pdb=" O ASN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.523A pdb=" N CYS A 663 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 236 Processing helix chain 'B' and resid 237 through 252 removed outlier: 4.068A pdb=" N GLY B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 287 removed outlier: 3.574A pdb=" N PHE B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Proline residue: B 282 - end of helix removed outlier: 4.066A pdb=" N THR B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.655A pdb=" N ILE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 388 Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.695A pdb=" N LEU B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 444 Proline residue: B 441 - end of helix removed outlier: 3.657A pdb=" N GLN B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 461 through 478 removed outlier: 3.571A pdb=" N TYR B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 542 " --> pdb=" O TYR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 558 Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 592 removed outlier: 3.580A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS B 589 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.523A pdb=" N CYS B 663 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 697 through 706 Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 237 through 252 removed outlier: 4.070A pdb=" N GLY C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 287 removed outlier: 3.574A pdb=" N PHE C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Proline residue: C 282 - end of helix removed outlier: 4.066A pdb=" N THR C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.656A pdb=" N ILE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 340 " --> pdb=" O MET C 336 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 388 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.695A pdb=" N LEU C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 444 Proline residue: C 441 - end of helix removed outlier: 3.658A pdb=" N GLN C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.572A pdb=" N TYR C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG C 526 " --> pdb=" O ASP C 522 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS C 542 " --> pdb=" O TYR C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 558 Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 592 removed outlier: 3.581A pdb=" N ILE C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS C 589 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 660 through 665 removed outlier: 3.522A pdb=" N CYS C 663 " --> pdb=" O GLY C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 697 Processing helix chain 'C' and resid 697 through 706 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 237 through 252 removed outlier: 4.069A pdb=" N GLY D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 287 removed outlier: 3.575A pdb=" N PHE D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Proline residue: D 282 - end of helix removed outlier: 4.066A pdb=" N THR D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 314 removed outlier: 4.327A pdb=" N TRP D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 351 removed outlier: 3.655A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 388 Processing helix chain 'D' and resid 391 through 407 removed outlier: 3.696A pdb=" N LEU D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 444 Proline residue: D 441 - end of helix removed outlier: 3.658A pdb=" N GLN D 444 " --> pdb=" O VAL D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 461 through 478 removed outlier: 3.572A pdb=" N TYR D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 520 removed outlier: 4.033A pdb=" N GLY D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS D 513 " --> pdb=" O MET D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 543 removed outlier: 3.738A pdb=" N ARG D 526 " --> pdb=" O ASP D 522 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS D 542 " --> pdb=" O TYR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 558 Processing helix chain 'D' and resid 566 through 574 removed outlier: 3.627A pdb=" N ILE D 570 " --> pdb=" O ASP D 566 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 574 " --> pdb=" O ILE D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.581A pdb=" N ILE D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS D 589 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU D 590 " --> pdb=" O ASN D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 609 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 660 through 665 removed outlier: 3.523A pdb=" N CYS D 663 " --> pdb=" O GLY D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 Processing helix chain 'D' and resid 697 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 617 Processing sheet with id=AA2, first strand: chain 'A' and resid 651 through 654 removed outlier: 3.609A pdb=" N SER A 673 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 613 through 617 Processing sheet with id=AA4, first strand: chain 'B' and resid 651 through 654 removed outlier: 3.610A pdb=" N SER B 673 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 613 through 617 Processing sheet with id=AA6, first strand: chain 'C' and resid 651 through 654 removed outlier: 3.610A pdb=" N SER C 673 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 613 through 617 Processing sheet with id=AA8, first strand: chain 'D' and resid 651 through 654 removed outlier: 3.609A pdb=" N SER D 673 " --> pdb=" O LEU D 644 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3081 1.33 - 1.45: 3873 1.45 - 1.57: 8634 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 15812 Sorted by residual: bond pdb=" N LEU B 665 " pdb=" CA LEU B 665 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" N LEU D 665 " pdb=" CA LEU D 665 " ideal model delta sigma weight residual 1.456 1.502 -0.047 1.35e-02 5.49e+03 1.20e+01 bond pdb=" N LEU A 665 " pdb=" CA LEU A 665 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.35e-02 5.49e+03 1.19e+01 bond pdb=" N LEU C 665 " pdb=" CA LEU C 665 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.35e-02 5.49e+03 1.16e+01 bond pdb=" N ILE B 399 " pdb=" CA ILE B 399 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.17e-02 7.31e+03 9.84e+00 ... (remaining 15807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 19154 1.97 - 3.95: 2036 3.95 - 5.92: 138 5.92 - 7.89: 15 7.89 - 9.87: 13 Bond angle restraints: 21356 Sorted by residual: angle pdb=" C ASN D 459 " pdb=" CA ASN D 459 " pdb=" CB ASN D 459 " ideal model delta sigma weight residual 110.19 120.06 -9.87 1.62e+00 3.81e-01 3.71e+01 angle pdb=" C ASN A 459 " pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " ideal model delta sigma weight residual 110.19 120.04 -9.85 1.62e+00 3.81e-01 3.70e+01 angle pdb=" C ASN C 459 " pdb=" CA ASN C 459 " pdb=" CB ASN C 459 " ideal model delta sigma weight residual 110.19 120.03 -9.84 1.62e+00 3.81e-01 3.69e+01 angle pdb=" C ASN B 459 " pdb=" CA ASN B 459 " pdb=" CB ASN B 459 " ideal model delta sigma weight residual 110.19 120.01 -9.82 1.62e+00 3.81e-01 3.67e+01 angle pdb=" CA HIS D 400 " pdb=" C HIS D 400 " pdb=" O HIS D 400 " ideal model delta sigma weight residual 120.82 115.77 5.05 1.05e+00 9.07e-01 2.31e+01 ... (remaining 21351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 8372 16.99 - 33.98: 836 33.98 - 50.97: 156 50.97 - 67.96: 44 67.96 - 84.95: 8 Dihedral angle restraints: 9416 sinusoidal: 3912 harmonic: 5504 Sorted by residual: dihedral pdb=" C ASN D 459 " pdb=" N ASN D 459 " pdb=" CA ASN D 459 " pdb=" CB ASN D 459 " ideal model delta harmonic sigma weight residual -122.60 -136.06 13.46 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" C ASN A 459 " pdb=" N ASN A 459 " pdb=" CA ASN A 459 " pdb=" CB ASN A 459 " ideal model delta harmonic sigma weight residual -122.60 -136.02 13.42 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" C ASN B 459 " pdb=" N ASN B 459 " pdb=" CA ASN B 459 " pdb=" CB ASN B 459 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 9413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1591 0.077 - 0.153: 605 0.153 - 0.230: 120 0.230 - 0.307: 8 0.307 - 0.384: 4 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA ASN D 459 " pdb=" N ASN D 459 " pdb=" C ASN D 459 " pdb=" CB ASN D 459 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA ASN A 459 " pdb=" N ASN A 459 " pdb=" C ASN A 459 " pdb=" CB ASN A 459 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN B 459 " pdb=" N ASN B 459 " pdb=" C ASN B 459 " pdb=" CB ASN B 459 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 2325 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 397 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C ARG D 397 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG D 397 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR D 398 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 397 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ARG A 397 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG A 397 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 397 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C ARG B 397 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG B 397 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR B 398 " -0.018 2.00e-02 2.50e+03 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5560 2.87 - 3.38: 14687 3.38 - 3.88: 24227 3.88 - 4.39: 26319 4.39 - 4.90: 46009 Nonbonded interactions: 116802 Sorted by model distance: nonbonded pdb=" N ASP A 326 " pdb=" OD1 ASP A 326 " model vdw 2.361 3.120 nonbonded pdb=" N ASP C 326 " pdb=" OD1 ASP C 326 " model vdw 2.361 3.120 nonbonded pdb=" N ASP B 326 " pdb=" OD1 ASP B 326 " model vdw 2.362 3.120 nonbonded pdb=" N ASP D 326 " pdb=" OD1 ASP D 326 " model vdw 2.362 3.120 nonbonded pdb=" O ASN A 459 " pdb=" OD1 ASN A 459 " model vdw 2.367 3.040 ... (remaining 116797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 14.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.010 0.070 15812 Z= 0.622 Angle : 1.163 9.867 21356 Z= 0.816 Chirality : 0.079 0.384 2328 Planarity : 0.008 0.075 2684 Dihedral : 14.026 84.953 5864 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.88 % Allowed : 12.53 % Favored : 86.59 % Cbeta Deviations : 0.23 % 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: -1.43 (0.18), residues: 1860 helix: -0.35 (0.14), residues: 1176 sheet: -1.13 (0.35), residues: 132 loop : -1.97 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 217 TYR 0.016 0.002 TYR D 556 PHE 0.020 0.002 PHE C 253 TRP 0.022 0.002 TRP A 451 HIS 0.006 0.002 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00984 (15812) covalent geometry : angle 1.16299 (21356) hydrogen bonds : bond 0.16158 ( 932) hydrogen bonds : angle 6.22300 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 291 time to evaluate : 0.603 Fit side-chains REVERT: A 433 ASP cc_start: 0.7950 (t0) cc_final: 0.7725 (t0) REVERT: A 679 TYR cc_start: 0.8133 (m-80) cc_final: 0.7878 (m-80) REVERT: A 696 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: B 433 ASP cc_start: 0.7981 (t0) cc_final: 0.7750 (t0) REVERT: B 460 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8305 (m-40) REVERT: B 696 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: C 433 ASP cc_start: 0.8020 (t0) cc_final: 0.7787 (t0) REVERT: C 460 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8277 (m-40) REVERT: C 696 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: D 433 ASP cc_start: 0.8007 (t0) cc_final: 0.7769 (t0) REVERT: D 460 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (m-40) outliers start: 15 outliers final: 8 residues processed: 306 average time/residue: 0.1297 time to fit residues: 58.5376 Evaluate side-chains 222 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 480 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 444 GLN A 455 ASN A 459 ASN A 460 ASN A 537 GLN A 586 ASN A 691 ASN B 245 GLN B 444 GLN B 455 ASN B 459 ASN B 519 GLN B 537 GLN B 603 ASN C 245 GLN C 444 GLN C 455 ASN C 459 ASN C 519 GLN C 537 GLN C 691 ASN D 245 GLN D 444 GLN D 455 ASN D 459 ASN D 519 GLN D 537 GLN D 603 ASN D 691 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.168694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130455 restraints weight = 21100.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132141 restraints weight = 11553.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132767 restraints weight = 9123.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133203 restraints weight = 7652.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133476 restraints weight = 7228.692| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15812 Z= 0.115 Angle : 0.545 6.401 21356 Z= 0.284 Chirality : 0.038 0.122 2328 Planarity : 0.005 0.049 2684 Dihedral : 6.205 77.441 2111 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.59 % Allowed : 14.53 % Favored : 82.88 % 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 (0.19), residues: 1860 helix: 1.44 (0.15), residues: 1132 sheet: -0.68 (0.38), residues: 132 loop : -1.29 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 588 TYR 0.009 0.001 TYR A 532 PHE 0.009 0.001 PHE B 659 TRP 0.011 0.001 TRP C 462 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00239 (15812) covalent geometry : angle 0.54454 (21356) hydrogen bonds : bond 0.04266 ( 932) hydrogen bonds : angle 4.02233 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.8495 (m-30) cc_final: 0.8186 (m-30) REVERT: A 273 LEU cc_start: 0.8625 (tp) cc_final: 0.8399 (tp) REVERT: A 433 ASP cc_start: 0.8053 (t0) cc_final: 0.7725 (t0) REVERT: B 222 MET cc_start: 0.6749 (mtt) cc_final: 0.6225 (mtm) REVERT: B 233 ARG cc_start: 0.7960 (tmm-80) cc_final: 0.7712 (ttt180) REVERT: B 433 ASP cc_start: 0.8034 (t0) cc_final: 0.7656 (t0) REVERT: C 222 MET cc_start: 0.6801 (mtt) cc_final: 0.6222 (mtm) REVERT: C 433 ASP cc_start: 0.8003 (t0) cc_final: 0.7627 (t0) REVERT: D 222 MET cc_start: 0.6682 (mtt) cc_final: 0.6181 (mtm) REVERT: D 233 ARG cc_start: 0.7982 (tmm-80) cc_final: 0.7724 (ttt180) REVERT: D 270 MET cc_start: 0.8312 (mmm) cc_final: 0.8072 (mmm) REVERT: D 273 LEU cc_start: 0.8592 (tp) cc_final: 0.8357 (tp) REVERT: D 433 ASP cc_start: 0.8094 (t0) cc_final: 0.7787 (t0) outliers start: 44 outliers final: 20 residues processed: 274 average time/residue: 0.1295 time to fit residues: 51.8820 Evaluate side-chains 235 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS B 586 ASN C 542 HIS C 586 ASN D 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125858 restraints weight = 21562.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124247 restraints weight = 15304.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125380 restraints weight = 12575.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126054 restraints weight = 9567.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126260 restraints weight = 8563.756| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15812 Z= 0.163 Angle : 0.558 7.970 21356 Z= 0.290 Chirality : 0.040 0.123 2328 Planarity : 0.004 0.044 2684 Dihedral : 4.853 49.798 2088 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.53 % Allowed : 15.41 % Favored : 82.06 % 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: 0.96 (0.20), residues: 1860 helix: 1.67 (0.16), residues: 1184 sheet: -0.48 (0.39), residues: 132 loop : -1.41 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 702 TYR 0.011 0.001 TYR C 468 PHE 0.019 0.002 PHE B 343 TRP 0.011 0.001 TRP A 494 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00379 (15812) covalent geometry : angle 0.55751 (21356) hydrogen bonds : bond 0.05249 ( 932) hydrogen bonds : angle 4.06107 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.8464 (m-30) cc_final: 0.8212 (m-30) REVERT: A 270 MET cc_start: 0.8323 (mmm) cc_final: 0.8086 (mmm) REVERT: B 233 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7748 (ttt180) REVERT: B 267 ASP cc_start: 0.8519 (m-30) cc_final: 0.8298 (m-30) REVERT: B 273 LEU cc_start: 0.8739 (tp) cc_final: 0.8465 (tp) REVERT: C 233 ARG cc_start: 0.8187 (tmm-80) cc_final: 0.7930 (ttt180) REVERT: C 273 LEU cc_start: 0.8698 (tp) cc_final: 0.8274 (tt) REVERT: D 233 ARG cc_start: 0.8212 (tmm-80) cc_final: 0.7892 (ttt180) outliers start: 43 outliers final: 25 residues processed: 269 average time/residue: 0.1263 time to fit residues: 49.9514 Evaluate side-chains 250 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 0.0670 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126353 restraints weight = 21460.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125478 restraints weight = 16017.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126817 restraints weight = 12154.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127474 restraints weight = 9195.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127647 restraints weight = 8431.191| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15812 Z= 0.132 Angle : 0.515 6.457 21356 Z= 0.268 Chirality : 0.038 0.119 2328 Planarity : 0.004 0.041 2684 Dihedral : 4.717 51.377 2088 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.94 % Allowed : 16.12 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1860 helix: 1.75 (0.16), residues: 1188 sheet: -0.07 (0.42), residues: 108 loop : -1.24 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 588 TYR 0.011 0.001 TYR A 468 PHE 0.008 0.001 PHE D 438 TRP 0.010 0.001 TRP B 451 HIS 0.003 0.001 HIS C 553 Details of bonding type rmsd covalent geometry : bond 0.00300 (15812) covalent geometry : angle 0.51519 (21356) hydrogen bonds : bond 0.04469 ( 932) hydrogen bonds : angle 3.93100 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 226 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 LEU cc_start: 0.8701 (tp) cc_final: 0.8447 (tp) REVERT: C 273 LEU cc_start: 0.8686 (tp) cc_final: 0.8410 (tp) REVERT: D 273 LEU cc_start: 0.8656 (tp) cc_final: 0.8417 (tp) outliers start: 67 outliers final: 46 residues processed: 265 average time/residue: 0.1234 time to fit residues: 48.8176 Evaluate side-chains 262 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 435 CYS Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 0.0970 chunk 131 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126439 restraints weight = 21497.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124779 restraints weight = 13329.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125919 restraints weight = 11283.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126660 restraints weight = 8846.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126713 restraints weight = 8300.933| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15812 Z= 0.156 Angle : 0.535 7.816 21356 Z= 0.280 Chirality : 0.039 0.127 2328 Planarity : 0.004 0.040 2684 Dihedral : 4.747 52.862 2088 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.35 % Allowed : 16.65 % 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: 1.18 (0.20), residues: 1860 helix: 1.76 (0.16), residues: 1188 sheet: -0.07 (0.42), residues: 108 loop : -1.16 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 391 TYR 0.011 0.001 TYR C 507 PHE 0.010 0.001 PHE B 659 TRP 0.011 0.001 TRP B 451 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00364 (15812) covalent geometry : angle 0.53533 (21356) hydrogen bonds : bond 0.04963 ( 932) hydrogen bonds : angle 3.99022 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 235 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8638 (tp) cc_final: 0.8169 (tt) REVERT: B 273 LEU cc_start: 0.8632 (tp) cc_final: 0.8377 (tp) REVERT: C 233 ARG cc_start: 0.8213 (tmm-80) cc_final: 0.7929 (ttt180) REVERT: C 273 LEU cc_start: 0.8620 (tp) cc_final: 0.8367 (tp) REVERT: D 233 ARG cc_start: 0.8196 (tmm-80) cc_final: 0.7984 (ttt180) REVERT: D 273 LEU cc_start: 0.8641 (tp) cc_final: 0.8181 (tt) outliers start: 74 outliers final: 57 residues processed: 283 average time/residue: 0.1171 time to fit residues: 49.6801 Evaluate side-chains 283 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 115 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129207 restraints weight = 21405.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129668 restraints weight = 13056.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130278 restraints weight = 10118.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.130994 restraints weight = 8766.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131086 restraints weight = 7387.393| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15812 Z= 0.109 Angle : 0.489 7.128 21356 Z= 0.253 Chirality : 0.038 0.122 2328 Planarity : 0.004 0.039 2684 Dihedral : 4.551 53.160 2088 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.76 % Allowed : 17.35 % Favored : 78.88 % 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: 1.63 (0.20), residues: 1860 helix: 2.12 (0.16), residues: 1156 sheet: 0.01 (0.42), residues: 108 loop : -0.82 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 588 TYR 0.018 0.001 TYR C 507 PHE 0.008 0.001 PHE A 659 TRP 0.008 0.001 TRP C 451 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00235 (15812) covalent geometry : angle 0.48902 (21356) hydrogen bonds : bond 0.03896 ( 932) hydrogen bonds : angle 3.82278 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 243 time to evaluate : 0.591 Fit side-chains REVERT: A 273 LEU cc_start: 0.8615 (tp) cc_final: 0.8344 (tp) REVERT: A 410 TYR cc_start: 0.8079 (m-80) cc_final: 0.7539 (m-80) REVERT: B 273 LEU cc_start: 0.8603 (tp) cc_final: 0.8368 (tp) REVERT: B 410 TYR cc_start: 0.8191 (m-80) cc_final: 0.7760 (m-80) REVERT: B 430 CYS cc_start: 0.8279 (m) cc_final: 0.7953 (m) REVERT: C 233 ARG cc_start: 0.8191 (tmm-80) cc_final: 0.7923 (ttt180) REVERT: C 273 LEU cc_start: 0.8603 (tp) cc_final: 0.8361 (tp) REVERT: C 410 TYR cc_start: 0.8146 (m-80) cc_final: 0.7635 (m-80) REVERT: D 233 ARG cc_start: 0.8197 (tmm-80) cc_final: 0.7897 (ttt180) REVERT: D 273 LEU cc_start: 0.8611 (tp) cc_final: 0.8352 (tp) REVERT: D 410 TYR cc_start: 0.8197 (m-80) cc_final: 0.7778 (m-80) REVERT: D 433 ASP cc_start: 0.8328 (t70) cc_final: 0.8070 (t0) outliers start: 64 outliers final: 45 residues processed: 278 average time/residue: 0.1122 time to fit residues: 47.3193 Evaluate side-chains 274 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 128 optimal weight: 0.0980 chunk 101 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126734 restraints weight = 21313.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125818 restraints weight = 14781.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126912 restraints weight = 12131.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127487 restraints weight = 9822.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127808 restraints weight = 8314.202| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15812 Z= 0.142 Angle : 0.525 6.364 21356 Z= 0.274 Chirality : 0.039 0.120 2328 Planarity : 0.004 0.040 2684 Dihedral : 4.601 52.768 2088 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.59 % Allowed : 17.41 % 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: 1.60 (0.20), residues: 1860 helix: 2.00 (0.16), residues: 1168 sheet: 0.08 (0.42), residues: 108 loop : -0.68 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 588 TYR 0.010 0.001 TYR A 507 PHE 0.009 0.001 PHE D 659 TRP 0.010 0.001 TRP C 494 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00328 (15812) covalent geometry : angle 0.52450 (21356) hydrogen bonds : bond 0.04540 ( 932) hydrogen bonds : angle 3.92632 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 0.582 Fit side-chains REVERT: A 273 LEU cc_start: 0.8628 (tp) cc_final: 0.8142 (tt) REVERT: A 410 TYR cc_start: 0.8125 (m-80) cc_final: 0.7616 (m-80) REVERT: B 273 LEU cc_start: 0.8617 (tp) cc_final: 0.8133 (tt) REVERT: B 410 TYR cc_start: 0.8228 (m-80) cc_final: 0.7789 (m-80) REVERT: B 430 CYS cc_start: 0.8269 (m) cc_final: 0.8051 (m) REVERT: C 233 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7943 (ttt180) REVERT: C 273 LEU cc_start: 0.8612 (tp) cc_final: 0.8331 (tp) REVERT: C 410 TYR cc_start: 0.8197 (m-80) cc_final: 0.7592 (m-80) REVERT: D 233 ARG cc_start: 0.8185 (tmm-80) cc_final: 0.7902 (ttt180) REVERT: D 273 LEU cc_start: 0.8639 (tp) cc_final: 0.8167 (tt) REVERT: D 333 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6827 (mtp85) REVERT: D 410 TYR cc_start: 0.8231 (m-80) cc_final: 0.7791 (m-80) outliers start: 61 outliers final: 49 residues processed: 277 average time/residue: 0.1260 time to fit residues: 51.8780 Evaluate side-chains 285 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127670 restraints weight = 21457.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126947 restraints weight = 13506.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127872 restraints weight = 11241.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128596 restraints weight = 9112.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128644 restraints weight = 7700.125| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15812 Z= 0.138 Angle : 0.526 7.934 21356 Z= 0.273 Chirality : 0.038 0.149 2328 Planarity : 0.004 0.038 2684 Dihedral : 4.588 52.341 2088 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.76 % Allowed : 16.88 % Favored : 79.35 % 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: 1.60 (0.20), residues: 1860 helix: 2.01 (0.16), residues: 1172 sheet: 0.11 (0.42), residues: 108 loop : -0.72 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 588 TYR 0.017 0.001 TYR D 507 PHE 0.009 0.001 PHE D 659 TRP 0.009 0.001 TRP B 451 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00321 (15812) covalent geometry : angle 0.52590 (21356) hydrogen bonds : bond 0.04445 ( 932) hydrogen bonds : angle 3.92253 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 1.060 Fit side-chains REVERT: A 273 LEU cc_start: 0.8613 (tp) cc_final: 0.8338 (tp) REVERT: B 273 LEU cc_start: 0.8612 (tp) cc_final: 0.8335 (tp) REVERT: B 410 TYR cc_start: 0.8199 (m-80) cc_final: 0.7805 (m-80) REVERT: C 273 LEU cc_start: 0.8588 (tp) cc_final: 0.8322 (tp) REVERT: D 273 LEU cc_start: 0.8630 (tp) cc_final: 0.8152 (tt) REVERT: D 410 TYR cc_start: 0.8206 (m-80) cc_final: 0.7814 (m-80) outliers start: 64 outliers final: 54 residues processed: 296 average time/residue: 0.1220 time to fit residues: 53.9573 Evaluate side-chains 291 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 80 optimal weight: 0.0980 chunk 46 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130195 restraints weight = 21482.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130124 restraints weight = 13529.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131083 restraints weight = 10390.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131872 restraints weight = 8700.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131840 restraints weight = 7390.513| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15812 Z= 0.109 Angle : 0.499 6.738 21356 Z= 0.258 Chirality : 0.038 0.118 2328 Planarity : 0.004 0.039 2684 Dihedral : 4.466 52.070 2088 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.29 % Allowed : 17.29 % Favored : 79.41 % 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: 1.75 (0.20), residues: 1860 helix: 2.12 (0.15), residues: 1172 sheet: 0.24 (0.42), residues: 108 loop : -0.67 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 588 TYR 0.023 0.001 TYR D 507 PHE 0.008 0.001 PHE C 659 TRP 0.008 0.001 TRP B 494 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00237 (15812) covalent geometry : angle 0.49913 (21356) hydrogen bonds : bond 0.03788 ( 932) hydrogen bonds : angle 3.83540 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 0.548 Fit side-chains REVERT: A 273 LEU cc_start: 0.8586 (tp) cc_final: 0.8338 (tp) REVERT: A 410 TYR cc_start: 0.7944 (m-80) cc_final: 0.7466 (m-80) REVERT: A 507 TYR cc_start: 0.8955 (t80) cc_final: 0.8666 (t80) REVERT: B 273 LEU cc_start: 0.8576 (tp) cc_final: 0.8323 (tp) REVERT: B 392 LEU cc_start: 0.8383 (tp) cc_final: 0.8008 (mt) REVERT: B 410 TYR cc_start: 0.8085 (m-80) cc_final: 0.7710 (m-80) REVERT: C 273 LEU cc_start: 0.8560 (tp) cc_final: 0.8303 (tp) REVERT: C 497 MET cc_start: 0.8631 (mmm) cc_final: 0.8184 (mtt) REVERT: D 273 LEU cc_start: 0.8609 (tp) cc_final: 0.8361 (tp) REVERT: D 410 TYR cc_start: 0.8085 (m-80) cc_final: 0.7729 (m-80) outliers start: 56 outliers final: 45 residues processed: 285 average time/residue: 0.1190 time to fit residues: 51.0507 Evaluate side-chains 285 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 50 optimal weight: 0.0670 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131568 restraints weight = 21517.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130990 restraints weight = 14535.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132094 restraints weight = 11794.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132783 restraints weight = 9133.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132973 restraints weight = 7854.948| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15812 Z= 0.105 Angle : 0.504 6.698 21356 Z= 0.259 Chirality : 0.038 0.126 2328 Planarity : 0.004 0.038 2684 Dihedral : 4.404 51.683 2088 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.76 % Allowed : 18.00 % Favored : 79.24 % 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: 1.91 (0.20), residues: 1860 helix: 2.22 (0.15), residues: 1172 sheet: 0.41 (0.43), residues: 108 loop : -0.58 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 588 TYR 0.009 0.001 TYR D 468 PHE 0.009 0.001 PHE C 343 TRP 0.009 0.001 TRP A 494 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00223 (15812) covalent geometry : angle 0.50393 (21356) hydrogen bonds : bond 0.03673 ( 932) hydrogen bonds : angle 3.79392 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 0.568 Fit side-chains REVERT: A 273 LEU cc_start: 0.8551 (tp) cc_final: 0.8316 (tp) REVERT: A 410 TYR cc_start: 0.7865 (m-80) cc_final: 0.7364 (m-80) REVERT: A 507 TYR cc_start: 0.8917 (t80) cc_final: 0.8650 (t80) REVERT: A 510 PHE cc_start: 0.8957 (t80) cc_final: 0.8684 (t80) REVERT: B 273 LEU cc_start: 0.8562 (tp) cc_final: 0.8321 (tp) REVERT: B 392 LEU cc_start: 0.8391 (tp) cc_final: 0.8018 (mt) REVERT: B 410 TYR cc_start: 0.7980 (m-80) cc_final: 0.7579 (m-80) REVERT: C 273 LEU cc_start: 0.8543 (tp) cc_final: 0.8288 (tp) REVERT: C 410 TYR cc_start: 0.7862 (m-80) cc_final: 0.7461 (m-80) REVERT: C 507 TYR cc_start: 0.8947 (t80) cc_final: 0.8621 (t80) REVERT: D 273 LEU cc_start: 0.8600 (tp) cc_final: 0.8353 (tp) REVERT: D 410 TYR cc_start: 0.7980 (m-80) cc_final: 0.7577 (m-80) REVERT: D 507 TYR cc_start: 0.8969 (t80) cc_final: 0.8675 (t80) outliers start: 47 outliers final: 44 residues processed: 289 average time/residue: 0.1208 time to fit residues: 52.3326 Evaluate side-chains 285 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127933 restraints weight = 21384.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128090 restraints weight = 15004.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128696 restraints weight = 11262.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129539 restraints weight = 9073.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.129757 restraints weight = 8091.687| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15812 Z= 0.144 Angle : 0.547 6.708 21356 Z= 0.283 Chirality : 0.039 0.135 2328 Planarity : 0.004 0.036 2684 Dihedral : 4.543 51.240 2088 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.71 % Allowed : 18.18 % Favored : 79.12 % 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 (0.20), residues: 1860 helix: 2.15 (0.15), residues: 1172 sheet: 0.33 (0.43), residues: 108 loop : -0.59 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 588 TYR 0.009 0.001 TYR B 468 PHE 0.010 0.001 PHE B 659 TRP 0.010 0.001 TRP D 451 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00333 (15812) covalent geometry : angle 0.54734 (21356) hydrogen bonds : bond 0.04552 ( 932) hydrogen bonds : angle 3.92990 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.24 seconds wall clock time: 39 minutes 51.10 seconds (2391.10 seconds total)