Starting phenix.real_space_refine on Sun Sep 13 06:21:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.cif" model { file = "/net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lgp_0882/09_2026/6lgp_0882.map" } resolution = 3.3 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 120 5.16 5 C 13940 2.51 5 N 3348 2.21 5 O 3784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21212 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5061 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 15, 'TRANS': 606} Chain breaks: 1 Chain: "B" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5061 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 15, 'TRANS': 606} Chain breaks: 1 Chain: "D" Number of atoms: 5061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5061 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 15, 'TRANS': 606} Chain breaks: 1 Chain: "A" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PLC': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PLC': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 242 Unusual residues: {'PLC': 3, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: C Time building chain proxies: 7.31, per 1000 atoms: 0.34 Number of scatterers: 21212 At special positions: 0 Unit cell: (152.25, 152.25, 130.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 20 15.00 O 3784 8.00 N 3348 7.00 C 13940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 131 " distance=0.00 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 146 " distance=0.00 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 171 " distance=0.00 Simple disulfide: pdb=" SG CYS C 271 " - pdb=" SG CYS C 271 " distance=0.00 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 446 " distance=0.00 Simple disulfide: pdb=" SG CYS C 496 " - pdb=" SG CYS C 496 " distance=0.00 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 550 " distance=0.00 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 612 " distance=0.00 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 619 " distance=0.00 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 721 " distance=0.00 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 731 " distance=0.00 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: 1.86 Conformation dependent library (CDL) restraints added in 761.3 milliseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 63.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 4.193A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.657A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.697A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.748A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.644A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.520A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.519A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 509 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 541 removed outlier: 3.661A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 565 removed outlier: 3.698A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 569 through 576 removed outlier: 3.893A pdb=" N SER A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.734A pdb=" N LYS A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 685 Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.782A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.661A pdb=" N PHE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.657A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.697A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.748A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.644A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.520A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.519A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 514 through 519 Processing helix chain 'B' and resid 520 through 541 removed outlier: 3.661A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 565 removed outlier: 3.698A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 569 through 576 removed outlier: 3.893A pdb=" N SER B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.734A pdb=" N LYS B 581 " --> pdb=" O VAL B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 685 Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.782A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.661A pdb=" N PHE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 131 through 148 Processing helix chain 'C' and resid 153 through 163 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.657A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.697A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 229 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.748A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.644A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.520A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.519A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 509 Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 520 through 541 removed outlier: 3.661A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 565 removed outlier: 3.698A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 569 through 576 removed outlier: 3.893A pdb=" N SER C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.734A pdb=" N LYS C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 685 Processing helix chain 'C' and resid 687 through 705 removed outlier: 3.782A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.661A pdb=" N PHE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 131 through 148 Processing helix chain 'D' and resid 153 through 163 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.657A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.697A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 229 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.748A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.644A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.520A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.519A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 514 through 519 Processing helix chain 'D' and resid 520 through 541 removed outlier: 3.661A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 565 removed outlier: 3.698A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 569 through 576 removed outlier: 3.893A pdb=" N SER D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.734A pdb=" N LYS D 581 " --> pdb=" O VAL D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 685 Processing helix chain 'D' and resid 687 through 705 removed outlier: 3.782A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.661A pdb=" N PHE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA2, first strand: chain 'A' and resid 722 through 724 removed outlier: 6.655A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA4, first strand: chain 'B' and resid 722 through 724 removed outlier: 6.655A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AA6, first strand: chain 'C' and resid 722 through 724 removed outlier: 6.655A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 378 Processing sheet with id=AA8, first strand: chain 'D' and resid 722 through 724 removed outlier: 6.655A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3204 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: 3.22 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3492 1.32 - 1.44: 5448 1.44 - 1.56: 12436 1.56 - 1.69: 40 1.69 - 1.81: 196 Bond restraints: 21612 Sorted by residual: bond pdb=" CA SER B 576 " pdb=" C SER B 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" CA SER C 576 " pdb=" C SER C 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" CA SER A 576 " pdb=" C SER A 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" CA SER D 576 " pdb=" C SER D 576 " ideal model delta sigma weight residual 1.522 1.465 0.056 1.72e-02 3.38e+03 1.08e+01 bond pdb=" O12 POV C 802 " pdb=" P POV C 802 " ideal model delta sigma weight residual 1.657 1.602 0.055 2.00e-02 2.50e+03 7.58e+00 ... (remaining 21607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 28284 2.21 - 4.41: 660 4.41 - 6.62: 80 6.62 - 8.83: 12 8.83 - 11.03: 12 Bond angle restraints: 29048 Sorted by residual: angle pdb=" N ILE D 199 " pdb=" CA ILE D 199 " pdb=" C ILE D 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N ILE B 199 " pdb=" CA ILE B 199 " pdb=" C ILE B 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N ILE C 199 " pdb=" CA ILE C 199 " pdb=" C ILE C 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N ILE A 199 " pdb=" CA ILE A 199 " pdb=" C ILE A 199 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" O3P PLC D 804 " pdb=" P PLC D 804 " pdb=" O4P PLC D 804 " ideal model delta sigma weight residual 93.62 104.65 -11.03 3.00e+00 1.11e-01 1.35e+01 ... (remaining 29043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 12672 35.49 - 70.98: 274 70.98 - 106.48: 16 106.48 - 141.97: 16 141.97 - 177.46: 8 Dihedral angle restraints: 12986 sinusoidal: 5650 harmonic: 7336 Sorted by residual: dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 131 " pdb=" CB CYS C 131 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS C 146 " pdb=" SG CYS C 146 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS C 171 " pdb=" SG CYS C 171 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 ... (remaining 12983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2844 0.068 - 0.137: 356 0.137 - 0.205: 8 0.205 - 0.274: 12 0.274 - 0.342: 4 Chirality restraints: 3224 Sorted by residual: chirality pdb=" C2 PLC D 805 " pdb=" C1 PLC D 805 " pdb=" C3 PLC D 805 " pdb=" O2 PLC D 805 " both_signs ideal model delta sigma weight residual False -2.31 -2.65 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C2 PLC A1003 " pdb=" C1 PLC A1003 " pdb=" C3 PLC A1003 " pdb=" O2 PLC A1003 " both_signs ideal model delta sigma weight residual False -2.31 -2.65 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C2 PLC C 804 " pdb=" C1 PLC C 804 " pdb=" C3 PLC C 804 " pdb=" O2 PLC C 804 " both_signs ideal model delta sigma weight residual False -2.31 -2.65 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 3221 not shown) Planarity restraints: 3536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1006 " 0.094 2.00e-02 2.50e+03 9.17e-02 8.40e+01 pdb=" C29 POV A1006 " -0.106 2.00e-02 2.50e+03 pdb="C210 POV A1006 " -0.076 2.00e-02 2.50e+03 pdb="C211 POV A1006 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 801 " -0.094 2.00e-02 2.50e+03 9.17e-02 8.40e+01 pdb=" C29 POV D 801 " 0.106 2.00e-02 2.50e+03 pdb="C210 POV D 801 " 0.076 2.00e-02 2.50e+03 pdb="C211 POV D 801 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 807 " -0.094 2.00e-02 2.50e+03 9.17e-02 8.40e+01 pdb=" C29 POV C 807 " 0.106 2.00e-02 2.50e+03 pdb="C210 POV C 807 " 0.076 2.00e-02 2.50e+03 pdb="C211 POV C 807 " -0.088 2.00e-02 2.50e+03 ... (remaining 3533 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 224 2.63 - 3.20: 19360 3.20 - 3.77: 30044 3.77 - 4.33: 43516 4.33 - 4.90: 73618 Nonbonded interactions: 166762 Sorted by model distance: nonbonded pdb=" OH TYR C 213 " pdb=" O PRO D 753 " model vdw 2.065 3.040 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR D 213 " model vdw 2.065 3.040 nonbonded pdb=" OH TYR B 213 " pdb=" O PRO C 753 " model vdw 2.065 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO B 753 " model vdw 2.065 3.040 nonbonded pdb=" O GLN B 514 " pdb=" OG SER B 518 " model vdw 2.184 3.040 ... (remaining 166757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 756 or (resid 1006 and (name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 310 or name C311 or name C312 or name C313 or name C314)))) selection = (chain 'B' and (resid 118 through 756 or resid 806)) selection = (chain 'C' and (resid 118 through 756 or resid 806)) selection = (chain 'D' and (resid 118 through 756 or resid 806)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.620 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.008 0.056 21612 Z= 0.372 Angle : 0.852 11.035 29059 Z= 0.462 Chirality : 0.048 0.342 3224 Planarity : 0.005 0.092 3536 Dihedral : 16.783 177.458 8204 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.65 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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: -4.33 (0.13), residues: 2472 helix: -2.16 (0.10), residues: 1572 sheet: -3.19 (0.45), residues: 84 loop : -4.07 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 712 TYR 0.024 0.002 TYR B 260 PHE 0.017 0.002 PHE A 316 TRP 0.029 0.002 TRP A 380 HIS 0.008 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00850 / 0.37 (21612) covalent geometry : angle 0.85179 / 0.46 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.18795 / 12.14 ( 1072) hydrogen bonds : angle 7.55811 / 5.27 ( 3204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.761 Fit side-chains REVERT: A 138 LEU cc_start: 0.7991 (mt) cc_final: 0.7690 (mt) REVERT: A 173 MET cc_start: 0.8576 (mtm) cc_final: 0.8205 (mtp) REVERT: A 211 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7793 (mp0) REVERT: A 655 LEU cc_start: 0.8535 (mm) cc_final: 0.8310 (mt) REVERT: A 687 GLU cc_start: 0.8438 (pp20) cc_final: 0.8060 (pp20) REVERT: A 714 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.7106 (ttm170) REVERT: A 738 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8525 (mtpp) REVERT: B 138 LEU cc_start: 0.7987 (mt) cc_final: 0.7686 (mt) REVERT: B 173 MET cc_start: 0.8574 (mtm) cc_final: 0.8206 (mtp) REVERT: B 211 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7791 (mp0) REVERT: B 655 LEU cc_start: 0.8537 (mm) cc_final: 0.8313 (mt) REVERT: B 687 GLU cc_start: 0.8434 (pp20) cc_final: 0.8060 (pp20) REVERT: B 714 ARG cc_start: 0.7560 (ttt-90) cc_final: 0.7107 (ttm170) REVERT: B 738 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8523 (mtpp) REVERT: C 138 LEU cc_start: 0.7994 (mt) cc_final: 0.7691 (mt) REVERT: C 173 MET cc_start: 0.8576 (mtm) cc_final: 0.8207 (mtp) REVERT: C 211 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7796 (mp0) REVERT: C 655 LEU cc_start: 0.8539 (mm) cc_final: 0.8313 (mt) REVERT: C 687 GLU cc_start: 0.8433 (pp20) cc_final: 0.8057 (pp20) REVERT: C 714 ARG cc_start: 0.7559 (ttt-90) cc_final: 0.7107 (ttm170) REVERT: C 738 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8520 (mtpp) REVERT: D 138 LEU cc_start: 0.7992 (mt) cc_final: 0.7687 (mt) REVERT: D 173 MET cc_start: 0.8570 (mtm) cc_final: 0.8195 (mtp) REVERT: D 211 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7793 (mp0) REVERT: D 655 LEU cc_start: 0.8540 (mm) cc_final: 0.8316 (mt) REVERT: D 687 GLU cc_start: 0.8438 (pp20) cc_final: 0.8059 (pp20) REVERT: D 714 ARG cc_start: 0.7558 (ttt-90) cc_final: 0.7103 (ttm170) REVERT: D 738 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8522 (mtpp) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1713 time to fit residues: 85.3206 Evaluate side-chains 260 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN A 244 HIS A 279 GLN A 297 ASN A 671 ASN A 683 ASN B 216 GLN B 244 HIS B 279 GLN B 297 ASN B 671 ASN B 683 ASN C 197 ASN C 216 GLN C 244 HIS C 279 GLN C 297 ASN C 671 ASN C 683 ASN D 197 ASN D 216 GLN D 244 HIS D 279 GLN D 297 ASN D 671 ASN D 683 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.141550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.104701 restraints weight = 24132.054| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.79 r_work: 0.2997 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21612 Z= 0.222 Angle : 0.692 11.723 29059 Z= 0.348 Chirality : 0.043 0.155 3224 Planarity : 0.004 0.034 3536 Dihedral : 13.670 175.135 3320 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 1.08 % Allowed : 15.52 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2472 helix: -0.41 (0.12), residues: 1588 sheet: -2.77 (0.46), residues: 84 loop : -3.67 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 327 TYR 0.026 0.002 TYR A 260 PHE 0.026 0.002 PHE D 193 TRP 0.026 0.002 TRP B 380 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (21612) covalent geometry : angle 0.69238 / 0.35 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.06442 / 4.22 ( 1072) hydrogen bonds : angle 4.94628 / 3.43 ( 3204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.696 Fit side-chains REVERT: A 122 ARG cc_start: 0.7540 (mtt180) cc_final: 0.6609 (mtp180) REVERT: A 138 LEU cc_start: 0.8027 (mt) cc_final: 0.7718 (mt) REVERT: A 173 MET cc_start: 0.8723 (mtm) cc_final: 0.8521 (mtp) REVERT: A 174 LYS cc_start: 0.8872 (tttt) cc_final: 0.8577 (tttm) REVERT: A 211 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8226 (mp0) REVERT: A 686 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8422 (mptt) REVERT: A 687 GLU cc_start: 0.8829 (pp20) cc_final: 0.8570 (pp20) REVERT: A 714 ARG cc_start: 0.7737 (ttt-90) cc_final: 0.7116 (ttm170) REVERT: B 122 ARG cc_start: 0.7617 (mtt180) cc_final: 0.6736 (mtp-110) REVERT: B 138 LEU cc_start: 0.8024 (mt) cc_final: 0.7715 (mt) REVERT: B 174 LYS cc_start: 0.8884 (tttt) cc_final: 0.8591 (tttm) REVERT: B 211 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8231 (mp0) REVERT: B 686 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8411 (mptt) REVERT: B 687 GLU cc_start: 0.8827 (pp20) cc_final: 0.8569 (pp20) REVERT: B 714 ARG cc_start: 0.7744 (ttt-90) cc_final: 0.7123 (ttm170) REVERT: C 122 ARG cc_start: 0.7619 (mtt180) cc_final: 0.6738 (mtp-110) REVERT: C 138 LEU cc_start: 0.8029 (mt) cc_final: 0.7715 (mt) REVERT: C 174 LYS cc_start: 0.8883 (tttt) cc_final: 0.8591 (tttm) REVERT: C 211 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8231 (mp0) REVERT: C 686 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8414 (mptt) REVERT: C 687 GLU cc_start: 0.8834 (pp20) cc_final: 0.8579 (pp20) REVERT: C 714 ARG cc_start: 0.7750 (ttt-90) cc_final: 0.7127 (ttm170) REVERT: D 122 ARG cc_start: 0.7614 (mtt180) cc_final: 0.6734 (mtp-110) REVERT: D 138 LEU cc_start: 0.8025 (mt) cc_final: 0.7712 (mt) REVERT: D 173 MET cc_start: 0.8728 (mtm) cc_final: 0.8523 (mtp) REVERT: D 174 LYS cc_start: 0.8880 (tttt) cc_final: 0.8585 (tttm) REVERT: D 211 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8218 (mp0) REVERT: D 686 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8406 (mptt) REVERT: D 687 GLU cc_start: 0.8826 (pp20) cc_final: 0.8564 (pp20) REVERT: D 714 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7116 (ttm170) outliers start: 24 outliers final: 12 residues processed: 301 average time/residue: 0.1619 time to fit residues: 72.5821 Evaluate side-chains 283 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 649 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 198 optimal weight: 0.0270 chunk 140 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 HIS B 745 HIS C 197 ASN C 745 HIS D 197 ASN D 745 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.147510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110890 restraints weight = 24130.871| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.84 r_work: 0.2970 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21612 Z= 0.119 Angle : 0.550 8.677 29059 Z= 0.279 Chirality : 0.038 0.152 3224 Planarity : 0.003 0.036 3536 Dihedral : 11.733 134.571 3320 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.81 % Allowed : 16.92 % Favored : 81.27 % 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: -1.23 (0.17), residues: 2472 helix: 0.56 (0.13), residues: 1596 sheet: -2.61 (0.47), residues: 84 loop : -3.58 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 696 TYR 0.011 0.001 TYR D 564 PHE 0.024 0.001 PHE D 193 TRP 0.018 0.002 TRP B 380 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (21612) covalent geometry : angle 0.54966 / 0.28 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.04179 / 2.77 ( 1072) hydrogen bonds : angle 4.29154 / 2.97 ( 3204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.765 Fit side-chains REVERT: A 122 ARG cc_start: 0.7649 (mtt180) cc_final: 0.6667 (mtp180) REVERT: A 159 MET cc_start: 0.7399 (tpp) cc_final: 0.7046 (tmm) REVERT: A 174 LYS cc_start: 0.8755 (tttt) cc_final: 0.8468 (tttp) REVERT: A 211 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8092 (mp0) REVERT: A 257 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7681 (pm20) REVERT: A 327 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.6881 (tpt170) REVERT: A 677 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8633 (mtp) REVERT: A 687 GLU cc_start: 0.8738 (pp20) cc_final: 0.8388 (pp20) REVERT: A 714 ARG cc_start: 0.7669 (ttt-90) cc_final: 0.7061 (ttm170) REVERT: B 122 ARG cc_start: 0.7461 (mtt180) cc_final: 0.6635 (mtp180) REVERT: B 138 LEU cc_start: 0.8161 (mt) cc_final: 0.7955 (mt) REVERT: B 159 MET cc_start: 0.7432 (tpp) cc_final: 0.7047 (tmm) REVERT: B 174 LYS cc_start: 0.8756 (tttt) cc_final: 0.8478 (tttp) REVERT: B 211 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8194 (mp0) REVERT: B 257 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7689 (pm20) REVERT: B 327 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.6887 (tpt170) REVERT: B 677 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8625 (mtp) REVERT: B 687 GLU cc_start: 0.8735 (pp20) cc_final: 0.8397 (pp20) REVERT: B 714 ARG cc_start: 0.7677 (ttt-90) cc_final: 0.7067 (ttm170) REVERT: C 122 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6651 (mtp180) REVERT: C 138 LEU cc_start: 0.8163 (mt) cc_final: 0.7956 (mt) REVERT: C 159 MET cc_start: 0.7440 (tpp) cc_final: 0.7051 (tmm) REVERT: C 174 LYS cc_start: 0.8764 (tttt) cc_final: 0.8492 (tttp) REVERT: C 211 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8202 (mp0) REVERT: C 257 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7700 (pm20) REVERT: C 327 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.6911 (tpt170) REVERT: C 677 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8636 (mtp) REVERT: C 687 GLU cc_start: 0.8747 (pp20) cc_final: 0.8410 (pp20) REVERT: C 714 ARG cc_start: 0.7700 (ttt-90) cc_final: 0.7087 (ttm170) REVERT: D 122 ARG cc_start: 0.7482 (mtt180) cc_final: 0.6649 (mtp180) REVERT: D 159 MET cc_start: 0.7423 (tpp) cc_final: 0.7059 (tmm) REVERT: D 174 LYS cc_start: 0.8749 (tttt) cc_final: 0.8466 (tttp) REVERT: D 211 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8099 (mp0) REVERT: D 257 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7693 (pm20) REVERT: D 327 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.6873 (tpt170) REVERT: D 677 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8638 (mtp) REVERT: D 687 GLU cc_start: 0.8746 (pp20) cc_final: 0.8403 (pp20) REVERT: D 714 ARG cc_start: 0.7682 (ttt-90) cc_final: 0.7065 (ttm170) outliers start: 40 outliers final: 16 residues processed: 340 average time/residue: 0.1659 time to fit residues: 83.8320 Evaluate side-chains 300 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 54 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 229 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.144361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.107420 restraints weight = 24380.984| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.85 r_work: 0.2935 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21612 Z= 0.146 Angle : 0.576 10.032 29059 Z= 0.289 Chirality : 0.040 0.335 3224 Planarity : 0.003 0.035 3536 Dihedral : 11.403 122.601 3320 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.35 % Allowed : 18.64 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2472 helix: 0.92 (0.13), residues: 1604 sheet: -2.38 (0.48), residues: 84 loop : -3.56 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.023 0.002 TYR D 260 PHE 0.017 0.001 PHE B 193 TRP 0.018 0.002 TRP A 380 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (21612) covalent geometry : angle 0.57582 / 0.29 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.04683 / 3.09 ( 1072) hydrogen bonds : angle 4.26443 / 2.95 ( 3204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 310 time to evaluate : 0.641 Fit side-chains REVERT: A 159 MET cc_start: 0.7676 (tpp) cc_final: 0.7317 (ttt) REVERT: A 160 HIS cc_start: 0.7371 (t-90) cc_final: 0.6875 (t-90) REVERT: A 174 LYS cc_start: 0.8784 (tttt) cc_final: 0.8453 (tttm) REVERT: A 179 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6573 (tp) REVERT: A 211 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8265 (mp0) REVERT: A 257 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7740 (pm20) REVERT: A 327 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.6850 (tpt170) REVERT: A 677 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8553 (mtp) REVERT: A 687 GLU cc_start: 0.8741 (pp20) cc_final: 0.8407 (pp20) REVERT: A 714 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.7025 (ttm170) REVERT: B 122 ARG cc_start: 0.7576 (mtt180) cc_final: 0.6590 (mtp180) REVERT: B 138 LEU cc_start: 0.7980 (mt) cc_final: 0.7760 (mt) REVERT: B 159 MET cc_start: 0.7679 (tpp) cc_final: 0.7312 (ttt) REVERT: B 160 HIS cc_start: 0.7354 (t-90) cc_final: 0.6861 (t-90) REVERT: B 174 LYS cc_start: 0.8789 (tttt) cc_final: 0.8398 (tttm) REVERT: B 179 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6567 (tp) REVERT: B 211 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8264 (mp0) REVERT: B 257 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7742 (pm20) REVERT: B 327 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.6854 (tpt170) REVERT: B 677 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8550 (mtp) REVERT: B 687 GLU cc_start: 0.8733 (pp20) cc_final: 0.8401 (pp20) REVERT: B 714 ARG cc_start: 0.7623 (ttt-90) cc_final: 0.7017 (ttm170) REVERT: C 122 ARG cc_start: 0.7584 (mtt180) cc_final: 0.6600 (mtp180) REVERT: C 138 LEU cc_start: 0.7973 (mt) cc_final: 0.7750 (mt) REVERT: C 159 MET cc_start: 0.7687 (tpp) cc_final: 0.7327 (ttt) REVERT: C 160 HIS cc_start: 0.7356 (t-90) cc_final: 0.6865 (t-90) REVERT: C 174 LYS cc_start: 0.8803 (tttt) cc_final: 0.8411 (tttm) REVERT: C 179 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6579 (tp) REVERT: C 211 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8268 (mp0) REVERT: C 257 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7752 (pm20) REVERT: C 327 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.6851 (tpt170) REVERT: C 677 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8559 (mtp) REVERT: C 687 GLU cc_start: 0.8752 (pp20) cc_final: 0.8419 (pp20) REVERT: C 714 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7056 (ttm170) REVERT: D 122 ARG cc_start: 0.7576 (mtt180) cc_final: 0.6615 (mtp180) REVERT: D 159 MET cc_start: 0.7695 (tpp) cc_final: 0.7323 (ttt) REVERT: D 160 HIS cc_start: 0.7367 (t-90) cc_final: 0.6873 (t-90) REVERT: D 174 LYS cc_start: 0.8783 (tttt) cc_final: 0.8449 (tttm) REVERT: D 179 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6576 (tp) REVERT: D 211 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8276 (mp0) REVERT: D 257 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7747 (pm20) REVERT: D 327 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.6848 (tpt170) REVERT: D 677 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8561 (mtp) REVERT: D 687 GLU cc_start: 0.8748 (pp20) cc_final: 0.8416 (pp20) REVERT: D 714 ARG cc_start: 0.7635 (ttt-90) cc_final: 0.7030 (ttm170) outliers start: 52 outliers final: 28 residues processed: 342 average time/residue: 0.1510 time to fit residues: 78.0591 Evaluate side-chains 330 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 294 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 237 optimal weight: 0.0980 chunk 130 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 231 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 HIS B 745 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.148336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111465 restraints weight = 24245.062| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.86 r_work: 0.2979 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21612 Z= 0.105 Angle : 0.533 9.872 29059 Z= 0.265 Chirality : 0.038 0.269 3224 Planarity : 0.003 0.038 3536 Dihedral : 10.661 109.313 3320 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.17 % Allowed : 19.04 % Favored : 78.79 % 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: -0.55 (0.17), residues: 2472 helix: 1.08 (0.13), residues: 1636 sheet: -2.18 (0.49), residues: 84 loop : -3.56 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 202 TYR 0.016 0.001 TYR D 260 PHE 0.018 0.001 PHE A 506 TRP 0.017 0.002 TRP B 380 HIS 0.005 0.001 HIS B 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (21612) covalent geometry : angle 0.53279 / 0.26 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.03849 / 2.55 ( 1072) hydrogen bonds : angle 4.05797 / 2.81 ( 3204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 0.631 Fit side-chains REVERT: A 160 HIS cc_start: 0.7316 (t-90) cc_final: 0.6863 (t-90) REVERT: A 174 LYS cc_start: 0.8692 (tttt) cc_final: 0.8374 (tttm) REVERT: A 211 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8263 (mp0) REVERT: A 229 ASP cc_start: 0.7530 (m-30) cc_final: 0.7301 (m-30) REVERT: A 260 TYR cc_start: 0.7912 (t80) cc_final: 0.7663 (t80) REVERT: A 327 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.6851 (tpt170) REVERT: A 677 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8557 (mtp) REVERT: A 687 GLU cc_start: 0.8652 (pp20) cc_final: 0.8385 (pp20) REVERT: A 714 ARG cc_start: 0.7603 (ttt-90) cc_final: 0.6997 (ttm170) REVERT: B 122 ARG cc_start: 0.7533 (mtt180) cc_final: 0.6554 (mtp180) REVERT: B 138 LEU cc_start: 0.7938 (mt) cc_final: 0.7720 (mt) REVERT: B 160 HIS cc_start: 0.7313 (t-90) cc_final: 0.6854 (t-90) REVERT: B 174 LYS cc_start: 0.8696 (tttt) cc_final: 0.8355 (tttm) REVERT: B 211 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8295 (mp0) REVERT: B 229 ASP cc_start: 0.7619 (m-30) cc_final: 0.7321 (m-30) REVERT: B 260 TYR cc_start: 0.7915 (t80) cc_final: 0.7670 (t80) REVERT: B 327 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.6847 (tpt170) REVERT: B 677 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8562 (mtp) REVERT: B 687 GLU cc_start: 0.8661 (pp20) cc_final: 0.8395 (pp20) REVERT: B 714 ARG cc_start: 0.7598 (ttt-90) cc_final: 0.6992 (ttm170) REVERT: C 122 ARG cc_start: 0.7544 (mtt180) cc_final: 0.6561 (mtp180) REVERT: C 138 LEU cc_start: 0.7930 (mt) cc_final: 0.7713 (mt) REVERT: C 159 MET cc_start: 0.7425 (tpp) cc_final: 0.6784 (tmm) REVERT: C 160 HIS cc_start: 0.7316 (t-90) cc_final: 0.6854 (t-90) REVERT: C 174 LYS cc_start: 0.8701 (tttt) cc_final: 0.8359 (tttm) REVERT: C 211 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8301 (mp0) REVERT: C 229 ASP cc_start: 0.7488 (m-30) cc_final: 0.7269 (m-30) REVERT: C 327 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.6844 (tpt170) REVERT: C 677 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: C 687 GLU cc_start: 0.8674 (pp20) cc_final: 0.8411 (pp20) REVERT: C 714 ARG cc_start: 0.7633 (ttt-90) cc_final: 0.7018 (ttm170) REVERT: D 122 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6286 (mtp180) REVERT: D 159 MET cc_start: 0.7412 (tpp) cc_final: 0.6775 (tmm) REVERT: D 160 HIS cc_start: 0.7325 (t-90) cc_final: 0.6867 (t-90) REVERT: D 174 LYS cc_start: 0.8680 (tttt) cc_final: 0.8357 (tttm) REVERT: D 185 GLU cc_start: 0.7706 (mp0) cc_final: 0.7183 (mp0) REVERT: D 211 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8279 (mp0) REVERT: D 229 ASP cc_start: 0.7535 (m-30) cc_final: 0.7298 (m-30) REVERT: D 327 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.6852 (tpt170) REVERT: D 677 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8565 (mtp) REVERT: D 687 GLU cc_start: 0.8663 (pp20) cc_final: 0.8398 (pp20) REVERT: D 714 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7002 (ttm170) outliers start: 48 outliers final: 32 residues processed: 346 average time/residue: 0.1645 time to fit residues: 84.6069 Evaluate side-chains 346 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 310 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 140 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 745 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.145714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.109946 restraints weight = 24080.165| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.76 r_work: 0.2960 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21612 Z= 0.138 Angle : 0.571 9.608 29059 Z= 0.283 Chirality : 0.040 0.251 3224 Planarity : 0.003 0.037 3536 Dihedral : 10.596 103.033 3320 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.44 % Allowed : 19.72 % Favored : 77.84 % 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: -0.43 (0.17), residues: 2472 helix: 1.22 (0.13), residues: 1612 sheet: -2.01 (0.51), residues: 84 loop : -3.49 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.021 0.001 TYR C 260 PHE 0.013 0.001 PHE C 506 TRP 0.014 0.002 TRP D 380 HIS 0.005 0.001 HIS B 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (21612) covalent geometry : angle 0.57115 / 0.28 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.04402 / 2.91 ( 1072) hydrogen bonds : angle 4.12059 / 2.85 ( 3204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.682 Fit side-chains REVERT: A 159 MET cc_start: 0.7273 (tpp) cc_final: 0.6973 (mtp) REVERT: A 160 HIS cc_start: 0.7290 (t-90) cc_final: 0.6878 (t-90) REVERT: A 174 LYS cc_start: 0.8685 (tttt) cc_final: 0.8288 (tttm) REVERT: A 185 GLU cc_start: 0.7698 (mp0) cc_final: 0.7187 (mp0) REVERT: A 202 ARG cc_start: 0.8840 (mtp-110) cc_final: 0.8564 (mtp85) REVERT: A 211 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8287 (mp0) REVERT: A 229 ASP cc_start: 0.7589 (m-30) cc_final: 0.7290 (m-30) REVERT: A 327 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.6831 (tpt170) REVERT: A 488 MET cc_start: 0.7422 (ttp) cc_final: 0.5459 (mmt) REVERT: A 677 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8554 (mtp) REVERT: A 687 GLU cc_start: 0.8688 (pp20) cc_final: 0.8341 (pp20) REVERT: A 714 ARG cc_start: 0.7607 (ttt-90) cc_final: 0.6995 (ttm170) REVERT: B 122 ARG cc_start: 0.7555 (mtt180) cc_final: 0.6557 (mtp180) REVERT: B 138 LEU cc_start: 0.7942 (mt) cc_final: 0.7720 (mt) REVERT: B 159 MET cc_start: 0.7302 (tpp) cc_final: 0.6990 (mtp) REVERT: B 160 HIS cc_start: 0.7298 (t-90) cc_final: 0.6879 (t-90) REVERT: B 174 LYS cc_start: 0.8682 (tttt) cc_final: 0.8336 (tttm) REVERT: B 185 GLU cc_start: 0.7718 (mp0) cc_final: 0.7210 (mp0) REVERT: B 202 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8569 (mtp85) REVERT: B 211 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8305 (mp0) REVERT: B 229 ASP cc_start: 0.7618 (m-30) cc_final: 0.7318 (m-30) REVERT: B 327 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.6836 (tpt170) REVERT: B 677 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8553 (mtp) REVERT: B 687 GLU cc_start: 0.8693 (pp20) cc_final: 0.8351 (pp20) REVERT: B 714 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.6998 (ttm170) REVERT: C 122 ARG cc_start: 0.7561 (mtt180) cc_final: 0.6567 (mtp180) REVERT: C 138 LEU cc_start: 0.7934 (mt) cc_final: 0.7713 (mt) REVERT: C 159 MET cc_start: 0.7370 (tpp) cc_final: 0.6941 (mtp) REVERT: C 160 HIS cc_start: 0.7295 (t-90) cc_final: 0.6862 (t-90) REVERT: C 174 LYS cc_start: 0.8693 (tttt) cc_final: 0.8346 (tttm) REVERT: C 185 GLU cc_start: 0.7718 (mp0) cc_final: 0.7209 (mp0) REVERT: C 202 ARG cc_start: 0.8848 (mtp-110) cc_final: 0.8556 (mtp85) REVERT: C 211 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8307 (mp0) REVERT: C 229 ASP cc_start: 0.7560 (m-30) cc_final: 0.7268 (m-30) REVERT: C 327 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.6834 (tpt170) REVERT: C 488 MET cc_start: 0.7434 (ttp) cc_final: 0.5467 (mmt) REVERT: C 677 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: C 687 GLU cc_start: 0.8699 (pp20) cc_final: 0.8356 (pp20) REVERT: C 714 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7021 (ttm170) REVERT: D 122 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6296 (mtp180) REVERT: D 159 MET cc_start: 0.7392 (tpp) cc_final: 0.6984 (mtp) REVERT: D 160 HIS cc_start: 0.7292 (t-90) cc_final: 0.6861 (t-90) REVERT: D 174 LYS cc_start: 0.8663 (tttt) cc_final: 0.8261 (tttm) REVERT: D 185 GLU cc_start: 0.7724 (mp0) cc_final: 0.7213 (mp0) REVERT: D 202 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8548 (mtp85) REVERT: D 211 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8302 (mp0) REVERT: D 229 ASP cc_start: 0.7592 (m-30) cc_final: 0.7292 (m-30) REVERT: D 327 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.6834 (tpt170) REVERT: D 488 MET cc_start: 0.7440 (ttp) cc_final: 0.5469 (mmt) REVERT: D 677 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: D 687 GLU cc_start: 0.8695 (pp20) cc_final: 0.8350 (pp20) REVERT: D 714 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.7000 (ttm170) outliers start: 54 outliers final: 36 residues processed: 341 average time/residue: 0.1698 time to fit residues: 86.8981 Evaluate side-chains 330 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 200 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 246 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.144453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.107660 restraints weight = 24292.168| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.85 r_work: 0.2931 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21612 Z= 0.157 Angle : 0.587 10.431 29059 Z= 0.292 Chirality : 0.040 0.220 3224 Planarity : 0.004 0.065 3536 Dihedral : 10.672 95.278 3320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.35 % Allowed : 20.49 % Favored : 77.17 % 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: -0.45 (0.17), residues: 2472 helix: 1.14 (0.13), residues: 1632 sheet: -2.01 (0.51), residues: 84 loop : -3.47 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.024 0.002 TYR C 260 PHE 0.014 0.001 PHE C 316 TRP 0.019 0.002 TRP C 380 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (21612) covalent geometry : angle 0.58733 / 0.29 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.04689 / 3.09 ( 1072) hydrogen bonds : angle 4.17009 / 2.89 ( 3204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.7336 (tpp) cc_final: 0.6837 (mtp) REVERT: A 160 HIS cc_start: 0.7264 (t-90) cc_final: 0.6896 (t-90) REVERT: A 174 LYS cc_start: 0.8743 (tttt) cc_final: 0.8414 (tttm) REVERT: A 185 GLU cc_start: 0.7706 (mp0) cc_final: 0.7202 (mp0) REVERT: A 202 ARG cc_start: 0.8846 (mtp-110) cc_final: 0.8090 (mtp85) REVERT: A 211 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8352 (mp0) REVERT: A 229 ASP cc_start: 0.7644 (m-30) cc_final: 0.7338 (m-30) REVERT: A 327 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.6901 (tpt170) REVERT: A 677 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8581 (mtp) REVERT: A 687 GLU cc_start: 0.8736 (pp20) cc_final: 0.8376 (pp20) REVERT: A 714 ARG cc_start: 0.7614 (ttt-90) cc_final: 0.6992 (ttm170) REVERT: B 138 LEU cc_start: 0.7885 (mt) cc_final: 0.7677 (mt) REVERT: B 159 MET cc_start: 0.7344 (tpp) cc_final: 0.6838 (mtp) REVERT: B 160 HIS cc_start: 0.7274 (t-90) cc_final: 0.6903 (t-90) REVERT: B 174 LYS cc_start: 0.8740 (tttt) cc_final: 0.8398 (tttm) REVERT: B 185 GLU cc_start: 0.7727 (mp0) cc_final: 0.7204 (mp0) REVERT: B 202 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8098 (mtp85) REVERT: B 211 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8371 (mp0) REVERT: B 229 ASP cc_start: 0.7657 (m-30) cc_final: 0.7353 (m-30) REVERT: B 327 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.6907 (tpt170) REVERT: B 488 MET cc_start: 0.7481 (ttp) cc_final: 0.5481 (mmt) REVERT: B 677 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: B 687 GLU cc_start: 0.8729 (pp20) cc_final: 0.8375 (pp20) REVERT: B 714 ARG cc_start: 0.7604 (ttt-90) cc_final: 0.6987 (ttm170) REVERT: C 138 LEU cc_start: 0.7877 (mt) cc_final: 0.7669 (mt) REVERT: C 159 MET cc_start: 0.7424 (tpp) cc_final: 0.6992 (mtp) REVERT: C 160 HIS cc_start: 0.7266 (t-90) cc_final: 0.6879 (t-90) REVERT: C 174 LYS cc_start: 0.8746 (tttt) cc_final: 0.8408 (tttm) REVERT: C 185 GLU cc_start: 0.7720 (mp0) cc_final: 0.7195 (mp0) REVERT: C 202 ARG cc_start: 0.8851 (mtp-110) cc_final: 0.8306 (mtp85) REVERT: C 211 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8375 (mp0) REVERT: C 229 ASP cc_start: 0.7612 (m-30) cc_final: 0.7323 (m-30) REVERT: C 327 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.6897 (tpt170) REVERT: C 677 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8583 (mtp) REVERT: C 687 GLU cc_start: 0.8735 (pp20) cc_final: 0.8383 (pp20) REVERT: C 714 ARG cc_start: 0.7637 (ttt-90) cc_final: 0.7009 (ttm170) REVERT: D 122 ARG cc_start: 0.7257 (mtt180) cc_final: 0.6266 (mtp180) REVERT: D 159 MET cc_start: 0.7416 (tpp) cc_final: 0.6993 (mtp) REVERT: D 160 HIS cc_start: 0.7267 (t-90) cc_final: 0.6883 (t-90) REVERT: D 174 LYS cc_start: 0.8733 (tttt) cc_final: 0.8399 (tttm) REVERT: D 185 GLU cc_start: 0.7721 (mp0) cc_final: 0.7217 (mp0) REVERT: D 202 ARG cc_start: 0.8845 (mtp-110) cc_final: 0.8295 (mtp85) REVERT: D 211 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8370 (mp0) REVERT: D 229 ASP cc_start: 0.7637 (m-30) cc_final: 0.7331 (m-30) REVERT: D 327 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.6892 (tpt170) REVERT: D 677 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8586 (mtp) REVERT: D 687 GLU cc_start: 0.8728 (pp20) cc_final: 0.8373 (pp20) REVERT: D 714 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.6988 (ttm170) outliers start: 52 outliers final: 40 residues processed: 329 average time/residue: 0.1714 time to fit residues: 84.6976 Evaluate side-chains 336 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 239 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.143394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107374 restraints weight = 24244.369| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.76 r_work: 0.2920 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21612 Z= 0.176 Angle : 0.615 11.080 29059 Z= 0.303 Chirality : 0.041 0.207 3224 Planarity : 0.004 0.056 3536 Dihedral : 10.881 88.418 3320 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.71 % Allowed : 20.85 % Favored : 76.44 % 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: -0.50 (0.17), residues: 2472 helix: 1.10 (0.13), residues: 1632 sheet: -1.96 (0.52), residues: 84 loop : -3.49 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.026 0.002 TYR D 260 PHE 0.016 0.002 PHE A 316 TRP 0.015 0.002 TRP C 380 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (21612) covalent geometry : angle 0.61512 / 0.30 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.05015 / 3.30 ( 1072) hydrogen bonds : angle 4.24100 / 2.94 ( 3204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 0.693 Fit side-chains REVERT: A 159 MET cc_start: 0.7107 (tpp) cc_final: 0.6886 (mtp) REVERT: A 160 HIS cc_start: 0.7233 (t-90) cc_final: 0.6903 (t-90) REVERT: A 174 LYS cc_start: 0.8682 (tttt) cc_final: 0.8337 (tttm) REVERT: A 202 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8251 (mtp85) REVERT: A 211 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8327 (mp0) REVERT: A 229 ASP cc_start: 0.7610 (m-30) cc_final: 0.7302 (m-30) REVERT: A 327 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.6928 (tpt170) REVERT: A 677 MET cc_start: 0.9025 (mtm) cc_final: 0.8565 (mtp) REVERT: A 687 GLU cc_start: 0.8707 (pp20) cc_final: 0.8333 (pp20) REVERT: B 138 LEU cc_start: 0.7872 (mt) cc_final: 0.7659 (mt) REVERT: B 159 MET cc_start: 0.7110 (tpp) cc_final: 0.6893 (mtp) REVERT: B 160 HIS cc_start: 0.7235 (t-90) cc_final: 0.6903 (t-90) REVERT: B 174 LYS cc_start: 0.8728 (tttt) cc_final: 0.8370 (tttm) REVERT: B 202 ARG cc_start: 0.8762 (mtp-110) cc_final: 0.8249 (mtp85) REVERT: B 211 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8326 (mp0) REVERT: B 229 ASP cc_start: 0.7629 (m-30) cc_final: 0.7323 (m-30) REVERT: B 327 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.6933 (tpt170) REVERT: B 677 MET cc_start: 0.9022 (mtm) cc_final: 0.8563 (mtp) REVERT: B 687 GLU cc_start: 0.8691 (pp20) cc_final: 0.8322 (pp20) REVERT: B 714 ARG cc_start: 0.7519 (ttt-90) cc_final: 0.6893 (ttm170) REVERT: C 138 LEU cc_start: 0.7851 (mt) cc_final: 0.7644 (mt) REVERT: C 159 MET cc_start: 0.7362 (tpp) cc_final: 0.7027 (mtp) REVERT: C 160 HIS cc_start: 0.7219 (t-90) cc_final: 0.6866 (t-90) REVERT: C 174 LYS cc_start: 0.8722 (tttt) cc_final: 0.8363 (tttm) REVERT: C 202 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8243 (mtp85) REVERT: C 211 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8328 (mp0) REVERT: C 229 ASP cc_start: 0.7561 (m-30) cc_final: 0.7267 (m-30) REVERT: C 327 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.6941 (tpt170) REVERT: C 677 MET cc_start: 0.9037 (mtm) cc_final: 0.8573 (mtp) REVERT: C 687 GLU cc_start: 0.8705 (pp20) cc_final: 0.8338 (pp20) REVERT: C 714 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.6914 (ttm170) REVERT: D 159 MET cc_start: 0.7362 (tpp) cc_final: 0.7020 (mtp) REVERT: D 160 HIS cc_start: 0.7210 (t-90) cc_final: 0.6857 (t-90) REVERT: D 174 LYS cc_start: 0.8682 (tttt) cc_final: 0.8337 (tttm) REVERT: D 179 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6398 (tp) REVERT: D 202 ARG cc_start: 0.8836 (mtp-110) cc_final: 0.8239 (mtp85) REVERT: D 211 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8341 (mp0) REVERT: D 229 ASP cc_start: 0.7611 (m-30) cc_final: 0.7305 (m-30) REVERT: D 327 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.6921 (tpt170) REVERT: D 677 MET cc_start: 0.9042 (mtm) cc_final: 0.8575 (mtp) REVERT: D 687 GLU cc_start: 0.8699 (pp20) cc_final: 0.8326 (pp20) REVERT: D 714 ARG cc_start: 0.7538 (ttt-90) cc_final: 0.6903 (ttm170) outliers start: 60 outliers final: 40 residues processed: 338 average time/residue: 0.1741 time to fit residues: 88.1274 Evaluate side-chains 332 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 351 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN C 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.148174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.111740 restraints weight = 24053.957| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.84 r_work: 0.2982 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21612 Z= 0.107 Angle : 0.553 9.480 29059 Z= 0.273 Chirality : 0.039 0.215 3224 Planarity : 0.003 0.048 3536 Dihedral : 10.326 83.289 3320 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.30 % Allowed : 20.35 % Favored : 77.35 % 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: -0.28 (0.17), residues: 2472 helix: 1.35 (0.13), residues: 1612 sheet: -1.99 (0.50), residues: 84 loop : -3.45 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 122 TYR 0.014 0.001 TYR C 260 PHE 0.009 0.001 PHE D 193 TRP 0.020 0.002 TRP C 380 HIS 0.004 0.001 HIS D 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (21612) covalent geometry : angle 0.55331 / 0.27 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.03854 / 2.55 ( 1072) hydrogen bonds : angle 4.07010 / 2.82 ( 3204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7188 (tpp) cc_final: 0.6886 (mtp) REVERT: A 160 HIS cc_start: 0.7182 (t-90) cc_final: 0.6864 (t-90) REVERT: A 174 LYS cc_start: 0.8692 (tttt) cc_final: 0.8439 (tttp) REVERT: A 179 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6374 (tp) REVERT: A 202 ARG cc_start: 0.8670 (mtp-110) cc_final: 0.7991 (mtm110) REVERT: A 211 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8329 (mp0) REVERT: A 327 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.6817 (tpt170) REVERT: A 577 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8714 (t) REVERT: A 677 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8573 (mtp) REVERT: A 687 GLU cc_start: 0.8709 (pp20) cc_final: 0.8365 (pp20) REVERT: A 719 GLU cc_start: 0.8111 (pm20) cc_final: 0.7868 (pm20) REVERT: B 159 MET cc_start: 0.7218 (tpp) cc_final: 0.6932 (mtp) REVERT: B 160 HIS cc_start: 0.7204 (t-90) cc_final: 0.6888 (t-90) REVERT: B 174 LYS cc_start: 0.8678 (tttt) cc_final: 0.8335 (tttm) REVERT: B 185 GLU cc_start: 0.7611 (mp0) cc_final: 0.7110 (mp0) REVERT: B 202 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8091 (mtm110) REVERT: B 211 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8337 (mp0) REVERT: B 327 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.6814 (tpt170) REVERT: B 488 MET cc_start: 0.6983 (ttp) cc_final: 0.6712 (ttm) REVERT: B 677 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8566 (mtp) REVERT: B 687 GLU cc_start: 0.8707 (pp20) cc_final: 0.8379 (pp20) REVERT: B 719 GLU cc_start: 0.8104 (pm20) cc_final: 0.7856 (pm20) REVERT: C 159 MET cc_start: 0.7353 (tpp) cc_final: 0.6942 (mtp) REVERT: C 160 HIS cc_start: 0.7224 (t-90) cc_final: 0.6846 (t-90) REVERT: C 174 LYS cc_start: 0.8688 (tttt) cc_final: 0.8341 (tttm) REVERT: C 185 GLU cc_start: 0.7603 (mp0) cc_final: 0.7121 (mp0) REVERT: C 202 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8080 (mtp85) REVERT: C 211 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8341 (mp0) REVERT: C 327 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.6815 (tpt170) REVERT: C 577 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8705 (t) REVERT: C 677 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: C 687 GLU cc_start: 0.8722 (pp20) cc_final: 0.8381 (pp20) REVERT: C 714 ARG cc_start: 0.7622 (ttt-90) cc_final: 0.6943 (ttm110) REVERT: C 719 GLU cc_start: 0.8088 (pm20) cc_final: 0.7871 (pm20) REVERT: D 159 MET cc_start: 0.7580 (tpp) cc_final: 0.7061 (mtp) REVERT: D 160 HIS cc_start: 0.7197 (t-90) cc_final: 0.6833 (t-90) REVERT: D 174 LYS cc_start: 0.8693 (tttt) cc_final: 0.8470 (tttp) REVERT: D 202 ARG cc_start: 0.8674 (mtp-110) cc_final: 0.8065 (mtp85) REVERT: D 211 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8330 (mp0) REVERT: D 327 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.6812 (tpt170) REVERT: D 677 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8579 (mtp) REVERT: D 687 GLU cc_start: 0.8709 (pp20) cc_final: 0.8381 (pp20) REVERT: D 719 GLU cc_start: 0.8095 (pm20) cc_final: 0.7848 (pm20) outliers start: 51 outliers final: 38 residues processed: 328 average time/residue: 0.1684 time to fit residues: 83.8385 Evaluate side-chains 332 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 103 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.148021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.111622 restraints weight = 24216.342| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.85 r_work: 0.2982 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21612 Z= 0.110 Angle : 0.551 8.839 29059 Z= 0.272 Chirality : 0.039 0.154 3224 Planarity : 0.003 0.047 3536 Dihedral : 10.116 80.683 3320 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.71 % Allowed : 21.39 % Favored : 76.90 % 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: -0.23 (0.17), residues: 2472 helix: 1.39 (0.13), residues: 1612 sheet: -1.89 (0.51), residues: 84 loop : -3.45 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 122 TYR 0.018 0.001 TYR A 260 PHE 0.008 0.001 PHE C 316 TRP 0.013 0.001 TRP C 380 HIS 0.004 0.001 HIS C 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (21612) covalent geometry : angle 0.55075 / 0.27 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.03890 / 2.57 ( 1072) hydrogen bonds : angle 4.05309 / 2.80 ( 3204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7271 (tpp) cc_final: 0.6929 (mtp) REVERT: A 160 HIS cc_start: 0.7186 (t-90) cc_final: 0.6879 (t-90) REVERT: A 174 LYS cc_start: 0.8667 (tttt) cc_final: 0.8463 (tttp) REVERT: A 179 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6341 (tp) REVERT: A 202 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8011 (mtm110) REVERT: A 211 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8321 (mp0) REVERT: A 327 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.6837 (tpt170) REVERT: A 577 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8744 (t) REVERT: A 677 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: A 687 GLU cc_start: 0.8682 (pp20) cc_final: 0.8413 (pp20) REVERT: A 714 ARG cc_start: 0.7614 (ttt-90) cc_final: 0.6935 (ttm110) REVERT: A 719 GLU cc_start: 0.8098 (pm20) cc_final: 0.7842 (pm20) REVERT: B 159 MET cc_start: 0.7223 (tpp) cc_final: 0.6871 (mtp) REVERT: B 160 HIS cc_start: 0.7193 (t-90) cc_final: 0.6885 (t-90) REVERT: B 174 LYS cc_start: 0.8647 (tttt) cc_final: 0.8343 (tttm) REVERT: B 202 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8019 (mtm110) REVERT: B 211 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8323 (mp0) REVERT: B 327 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.6836 (tpt170) REVERT: B 488 MET cc_start: 0.6863 (ttp) cc_final: 0.6573 (ttm) REVERT: B 577 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8740 (t) REVERT: B 677 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8551 (mtp) REVERT: B 687 GLU cc_start: 0.8683 (pp20) cc_final: 0.8410 (pp20) REVERT: B 714 ARG cc_start: 0.7610 (ttt-90) cc_final: 0.6941 (ttm110) REVERT: C 159 MET cc_start: 0.7368 (tpp) cc_final: 0.6983 (mtp) REVERT: C 160 HIS cc_start: 0.7193 (t-90) cc_final: 0.6836 (t-90) REVERT: C 174 LYS cc_start: 0.8649 (tttt) cc_final: 0.8307 (tttm) REVERT: C 202 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8192 (mtp85) REVERT: C 211 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8337 (mp0) REVERT: C 327 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.6840 (tpt170) REVERT: C 577 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8738 (t) REVERT: C 677 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8554 (mtp) REVERT: C 687 GLU cc_start: 0.8696 (pp20) cc_final: 0.8424 (pp20) REVERT: C 714 ARG cc_start: 0.7625 (ttt-90) cc_final: 0.6946 (ttm110) REVERT: C 719 GLU cc_start: 0.8077 (pm20) cc_final: 0.7824 (pm20) REVERT: D 159 MET cc_start: 0.7354 (tpp) cc_final: 0.6980 (mtp) REVERT: D 160 HIS cc_start: 0.7192 (t-90) cc_final: 0.6839 (t-90) REVERT: D 174 LYS cc_start: 0.8655 (tttt) cc_final: 0.8435 (tttp) REVERT: D 202 ARG cc_start: 0.8657 (mtp-110) cc_final: 0.8165 (mtp85) REVERT: D 211 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8318 (mp0) REVERT: D 327 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.6834 (tpt170) REVERT: D 577 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8737 (t) REVERT: D 677 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8561 (mtp) REVERT: D 687 GLU cc_start: 0.8690 (pp20) cc_final: 0.8417 (pp20) REVERT: D 714 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.6934 (ttm110) REVERT: D 719 GLU cc_start: 0.8079 (pm20) cc_final: 0.7824 (pm20) outliers start: 38 outliers final: 29 residues processed: 303 average time/residue: 0.1820 time to fit residues: 82.6090 Evaluate side-chains 320 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 132 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 29 optimal weight: 0.0020 chunk 234 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 153 optimal weight: 0.0470 chunk 143 optimal weight: 5.9990 overall best weight: 0.5286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 ASN C 251 ASN D 251 ASN D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.151393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.115517 restraints weight = 24112.608| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.83 r_work: 0.3098 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21612 Z= 0.097 Angle : 0.526 8.662 29059 Z= 0.261 Chirality : 0.038 0.155 3224 Planarity : 0.003 0.048 3536 Dihedral : 9.674 74.976 3320 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.81 % Allowed : 21.62 % Favored : 76.58 % 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: -0.14 (0.17), residues: 2472 helix: 1.55 (0.13), residues: 1580 sheet: -1.87 (0.51), residues: 84 loop : -3.46 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.010 0.001 TYR A 321 PHE 0.009 0.001 PHE C 193 TRP 0.014 0.001 TRP C 380 HIS 0.004 0.001 HIS C 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (21612) covalent geometry : angle 0.52620 / 0.26 (29048) SS BOND : angle 0.00000 / 0.00 ( 11) hydrogen bonds : bond 0.03438 / 2.28 ( 1072) hydrogen bonds : angle 3.93317 / 2.72 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5268.77 seconds wall clock time: 91 minutes 0.28 seconds (5460.28 seconds total)