Starting phenix.real_space_refine on Thu Mar 5 10:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lgp_0882/03_2026/6lgp_0882.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lgp_0882/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6lgp_0882/03_2026/6lgp_0882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lgp_0882/03_2026/6lgp_0882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lgp_0882/03_2026/6lgp_0882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lgp_0882/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 82 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: 82 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: 82 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: 7.24, 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: 1.57 Conformation dependent library (CDL) restraints added in 949.8 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: 0.58 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: 2.20 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: 12810 35.49 - 70.98: 308 70.98 - 106.48: 28 106.48 - 141.97: 32 141.97 - 177.46: 8 Dihedral angle restraints: 13186 sinusoidal: 5850 harmonic: 7336 Sorted by residual: dihedral pdb=" C1B PLC A1002 " pdb=" CB PLC A1002 " pdb=" O3 PLC A1002 " pdb=" C3 PLC A1002 " ideal model delta sinusoidal sigma weight residual 181.23 3.77 177.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1B PLC D 804 " pdb=" CB PLC D 804 " pdb=" O3 PLC D 804 " pdb=" C3 PLC D 804 " ideal model delta sinusoidal sigma weight residual 181.23 3.77 177.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1B PLC B 803 " pdb=" CB PLC B 803 " pdb=" O3 PLC B 803 " pdb=" C3 PLC B 803 " ideal model delta sinusoidal sigma weight residual 181.23 3.77 177.46 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13183 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: 0.02 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.200 Find NCS groups from input model: 0.550 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 18.349 177.458 8404 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 covalent geometry : bond 0.00850 (21612) covalent geometry : angle 0.85179 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.18795 ( 1072) hydrogen bonds : angle 7.55811 ( 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 : 0.858 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: 0.1760 time to fit residues: 86.0121 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 : 0.672 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 216 GLN C 244 HIS C 279 GLN C 297 ASN C 671 ASN C 683 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.140951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.103522 restraints weight = 24171.085| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.85 r_work: 0.2864 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21612 Z= 0.222 Angle : 0.696 11.699 29059 Z= 0.349 Chirality : 0.043 0.159 3224 Planarity : 0.004 0.035 3536 Dihedral : 15.970 137.852 3520 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 1.08 % Allowed : 15.34 % Favored : 83.57 % 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: -2.28 (0.16), residues: 2472 helix: -0.39 (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 0.003 0.000 ARG D 327 TYR 0.026 0.002 TYR D 260 PHE 0.026 0.002 PHE A 193 TRP 0.026 0.002 TRP B 380 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00538 (21612) covalent geometry : angle 0.69613 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.06402 ( 1072) hydrogen bonds : angle 4.93041 ( 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 304 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.731 Fit side-chains REVERT: A 122 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6590 (mtp180) REVERT: A 138 LEU cc_start: 0.7971 (mt) cc_final: 0.7663 (mt) REVERT: A 173 MET cc_start: 0.8688 (mtm) cc_final: 0.8461 (mtp) REVERT: A 174 LYS cc_start: 0.8790 (tttt) cc_final: 0.8479 (tttm) REVERT: A 211 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8267 (mp0) REVERT: A 686 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8402 (mptt) REVERT: A 687 GLU cc_start: 0.8826 (pp20) cc_final: 0.8555 (pp20) REVERT: A 704 GLU cc_start: 0.7767 (tt0) cc_final: 0.7518 (tt0) REVERT: A 714 ARG cc_start: 0.7695 (ttt-90) cc_final: 0.7067 (ttm170) REVERT: B 122 ARG cc_start: 0.7597 (mtt180) cc_final: 0.6759 (mtp-110) REVERT: B 138 LEU cc_start: 0.7971 (mt) cc_final: 0.7660 (mt) REVERT: B 173 MET cc_start: 0.8692 (mtm) cc_final: 0.8473 (mtp) REVERT: B 174 LYS cc_start: 0.8799 (tttt) cc_final: 0.8487 (tttm) REVERT: B 211 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8270 (mp0) REVERT: B 276 GLU cc_start: 0.7506 (pm20) cc_final: 0.7301 (pm20) REVERT: B 686 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8399 (mptt) REVERT: B 687 GLU cc_start: 0.8819 (pp20) cc_final: 0.8550 (pp20) REVERT: B 704 GLU cc_start: 0.7777 (tt0) cc_final: 0.7526 (tt0) REVERT: B 714 ARG cc_start: 0.7708 (ttt-90) cc_final: 0.7079 (ttm170) REVERT: C 122 ARG cc_start: 0.7449 (mtt180) cc_final: 0.6573 (mtp-110) REVERT: C 138 LEU cc_start: 0.7979 (mt) cc_final: 0.7666 (mt) REVERT: C 173 MET cc_start: 0.8697 (mtm) cc_final: 0.8478 (mtp) REVERT: C 174 LYS cc_start: 0.8802 (tttt) cc_final: 0.8492 (tttm) REVERT: C 211 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8274 (mp0) REVERT: C 686 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8395 (mptt) REVERT: C 687 GLU cc_start: 0.8823 (pp20) cc_final: 0.8555 (pp20) REVERT: C 704 GLU cc_start: 0.7787 (tt0) cc_final: 0.7536 (tt0) REVERT: C 714 ARG cc_start: 0.7717 (ttt-90) cc_final: 0.7082 (ttm170) REVERT: D 122 ARG cc_start: 0.7446 (mtt180) cc_final: 0.6572 (mtp-110) REVERT: D 138 LEU cc_start: 0.7978 (mt) cc_final: 0.7664 (mt) REVERT: D 173 MET cc_start: 0.8695 (mtm) cc_final: 0.8474 (mtp) REVERT: D 174 LYS cc_start: 0.8805 (tttt) cc_final: 0.8495 (tttm) REVERT: D 211 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8266 (mp0) REVERT: D 686 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8386 (mptt) REVERT: D 687 GLU cc_start: 0.8814 (pp20) cc_final: 0.8543 (pp20) REVERT: D 704 GLU cc_start: 0.7790 (tt0) cc_final: 0.7541 (tt0) REVERT: D 714 ARG cc_start: 0.7707 (ttt-90) cc_final: 0.7074 (ttm170) outliers start: 24 outliers final: 12 residues processed: 300 average time/residue: 0.1667 time to fit residues: 73.8755 Evaluate side-chains 284 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 272 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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: 0.8980 chunk 204 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 HIS B 745 HIS C 745 HIS D 745 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.146935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.110122 restraints weight = 24090.559| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.85 r_work: 0.3002 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21612 Z= 0.115 Angle : 0.551 9.256 29059 Z= 0.281 Chirality : 0.038 0.150 3224 Planarity : 0.003 0.036 3536 Dihedral : 14.249 131.989 3520 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 1.85 % Allowed : 17.06 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2472 helix: 0.58 (0.13), residues: 1596 sheet: -2.65 (0.46), residues: 84 loop : -3.59 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 327 TYR 0.012 0.001 TYR A 260 PHE 0.021 0.001 PHE A 193 TRP 0.019 0.002 TRP B 380 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00240 (21612) covalent geometry : angle 0.55128 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.04292 ( 1072) hydrogen bonds : angle 4.32910 ( 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 361 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 320 time to evaluate : 0.704 Fit side-chains REVERT: A 122 ARG cc_start: 0.7682 (mtt180) cc_final: 0.6708 (mtp180) REVERT: A 159 MET cc_start: 0.7598 (tpp) cc_final: 0.7232 (tmm) REVERT: A 174 LYS cc_start: 0.8853 (tttt) cc_final: 0.8578 (tttp) REVERT: A 211 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8167 (mp0) REVERT: A 257 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7725 (pm20) REVERT: A 327 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.6920 (tpt170) REVERT: A 677 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8733 (mtp) REVERT: A 687 GLU cc_start: 0.8773 (pp20) cc_final: 0.8480 (pp20) REVERT: A 704 GLU cc_start: 0.7587 (tt0) cc_final: 0.7244 (tt0) REVERT: A 714 ARG cc_start: 0.7708 (ttt-90) cc_final: 0.7099 (ttm170) REVERT: B 122 ARG cc_start: 0.7502 (mtt180) cc_final: 0.6676 (mtp180) REVERT: B 138 LEU cc_start: 0.8216 (mt) cc_final: 0.8015 (mt) REVERT: B 159 MET cc_start: 0.7606 (tpp) cc_final: 0.7241 (tmm) REVERT: B 174 LYS cc_start: 0.8852 (tttt) cc_final: 0.8573 (tttp) REVERT: B 211 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8182 (mp0) REVERT: B 257 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7728 (pm20) REVERT: B 276 GLU cc_start: 0.7735 (pm20) cc_final: 0.7484 (pm20) REVERT: B 327 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.6906 (tpt170) REVERT: B 677 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8727 (mtp) REVERT: B 687 GLU cc_start: 0.8771 (pp20) cc_final: 0.8482 (pp20) REVERT: B 704 GLU cc_start: 0.7602 (tt0) cc_final: 0.7261 (tt0) REVERT: B 714 ARG cc_start: 0.7716 (ttt-90) cc_final: 0.7101 (ttm170) REVERT: C 122 ARG cc_start: 0.7512 (mtt180) cc_final: 0.6689 (mtp180) REVERT: C 138 LEU cc_start: 0.8219 (mt) cc_final: 0.8016 (mt) REVERT: C 159 MET cc_start: 0.7615 (tpp) cc_final: 0.7244 (tmm) REVERT: C 174 LYS cc_start: 0.8858 (tttt) cc_final: 0.8586 (tttp) REVERT: C 211 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8185 (mp0) REVERT: C 257 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7738 (pm20) REVERT: C 327 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.6910 (tpt170) REVERT: C 677 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8731 (mtp) REVERT: C 687 GLU cc_start: 0.8780 (pp20) cc_final: 0.8492 (pp20) REVERT: C 704 GLU cc_start: 0.7598 (tt0) cc_final: 0.7254 (tt0) REVERT: C 714 ARG cc_start: 0.7740 (ttt-90) cc_final: 0.7121 (ttm170) REVERT: D 122 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6693 (mtp180) REVERT: D 138 LEU cc_start: 0.8224 (mt) cc_final: 0.8022 (mt) REVERT: D 159 MET cc_start: 0.7627 (tpp) cc_final: 0.7253 (tmm) REVERT: D 174 LYS cc_start: 0.8848 (tttt) cc_final: 0.8572 (tttp) REVERT: D 211 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8180 (mp0) REVERT: D 257 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7741 (pm20) REVERT: D 327 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.6913 (tpt170) REVERT: D 677 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8734 (mtp) REVERT: D 687 GLU cc_start: 0.8784 (pp20) cc_final: 0.8496 (pp20) REVERT: D 704 GLU cc_start: 0.7604 (tt0) cc_final: 0.7261 (tt0) REVERT: D 714 ARG cc_start: 0.7732 (ttt-90) cc_final: 0.7122 (ttm170) outliers start: 41 outliers final: 13 residues processed: 353 average time/residue: 0.1654 time to fit residues: 86.4818 Evaluate side-chains 305 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 288 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 508 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 373 LEU 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 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 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: 0.9990 chunk 189 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.106899 restraints weight = 24305.180| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.85 r_work: 0.2918 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2302 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= 0.156 Angle : 0.596 10.374 29059 Z= 0.294 Chirality : 0.041 0.315 3224 Planarity : 0.003 0.035 3536 Dihedral : 13.904 112.127 3520 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.35 % Allowed : 18.23 % Favored : 79.42 % 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: -0.90 (0.17), residues: 2472 helix: 0.80 (0.13), residues: 1628 sheet: -2.42 (0.48), residues: 84 loop : -3.61 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 202 TYR 0.024 0.002 TYR A 260 PHE 0.016 0.001 PHE B 193 TRP 0.018 0.002 TRP B 380 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00364 (21612) covalent geometry : angle 0.59630 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.04820 ( 1072) hydrogen bonds : angle 4.29144 ( 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 359 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 0.756 Fit side-chains REVERT: A 159 MET cc_start: 0.7649 (tpp) cc_final: 0.7289 (ttt) REVERT: A 160 HIS cc_start: 0.7361 (t-90) cc_final: 0.6866 (t-90) REVERT: A 174 LYS cc_start: 0.8769 (tttt) cc_final: 0.8442 (tttm) REVERT: A 179 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6583 (tp) REVERT: A 211 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8261 (mp0) REVERT: A 257 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7728 (pm20) REVERT: A 327 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.6756 (tmt-80) REVERT: A 677 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8549 (mtp) REVERT: A 687 GLU cc_start: 0.8726 (pp20) cc_final: 0.8385 (pp20) REVERT: A 704 GLU cc_start: 0.7606 (tt0) cc_final: 0.7286 (tt0) REVERT: A 714 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.7002 (ttm170) REVERT: B 122 ARG cc_start: 0.7568 (mtt180) cc_final: 0.6586 (mtp180) REVERT: B 138 LEU cc_start: 0.7956 (mt) cc_final: 0.7734 (mt) REVERT: B 159 MET cc_start: 0.7663 (tpp) cc_final: 0.7295 (ttt) REVERT: B 160 HIS cc_start: 0.7357 (t-90) cc_final: 0.6859 (t-90) REVERT: B 174 LYS cc_start: 0.8765 (tttt) cc_final: 0.8483 (tttp) REVERT: B 179 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6590 (tp) REVERT: B 211 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8281 (mp0) REVERT: B 257 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7729 (pm20) REVERT: B 276 GLU cc_start: 0.7739 (pm20) cc_final: 0.7470 (pm20) REVERT: B 327 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.6750 (tmt-80) REVERT: B 677 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8545 (mtp) REVERT: B 687 GLU cc_start: 0.8726 (pp20) cc_final: 0.8389 (pp20) REVERT: B 704 GLU cc_start: 0.7624 (tt0) cc_final: 0.7306 (tt0) REVERT: B 714 ARG cc_start: 0.7612 (ttt-90) cc_final: 0.7007 (ttm170) REVERT: C 122 ARG cc_start: 0.7586 (mtt180) cc_final: 0.6598 (mtp180) REVERT: C 138 LEU cc_start: 0.7960 (mt) cc_final: 0.7736 (mt) REVERT: C 159 MET cc_start: 0.7662 (tpp) cc_final: 0.7305 (ttt) REVERT: C 160 HIS cc_start: 0.7353 (t-90) cc_final: 0.6853 (t-90) REVERT: C 174 LYS cc_start: 0.8774 (tttt) cc_final: 0.8449 (tttm) REVERT: C 179 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6604 (tp) REVERT: C 211 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8280 (mp0) REVERT: C 257 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7735 (pm20) REVERT: C 327 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.6754 (tmt-80) REVERT: C 677 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8550 (mtp) REVERT: C 687 GLU cc_start: 0.8731 (pp20) cc_final: 0.8393 (pp20) REVERT: C 704 GLU cc_start: 0.7602 (tt0) cc_final: 0.7252 (tt0) REVERT: C 714 ARG cc_start: 0.7643 (ttt-90) cc_final: 0.7025 (ttm170) REVERT: D 122 ARG cc_start: 0.7589 (mtt180) cc_final: 0.6602 (mtp180) REVERT: D 138 LEU cc_start: 0.7967 (mt) cc_final: 0.7744 (mt) REVERT: D 159 MET cc_start: 0.7661 (tpp) cc_final: 0.7295 (ttt) REVERT: D 160 HIS cc_start: 0.7353 (t-90) cc_final: 0.6857 (t-90) REVERT: D 174 LYS cc_start: 0.8761 (tttt) cc_final: 0.8436 (tttm) REVERT: D 179 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6593 (tp) REVERT: D 211 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8274 (mp0) REVERT: D 257 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7738 (pm20) REVERT: D 327 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.6753 (tmt-80) REVERT: D 677 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: D 687 GLU cc_start: 0.8734 (pp20) cc_final: 0.8396 (pp20) REVERT: D 704 GLU cc_start: 0.7620 (tt0) cc_final: 0.7273 (tt0) REVERT: D 714 ARG cc_start: 0.7623 (ttt-90) cc_final: 0.7007 (ttm170) outliers start: 52 outliers final: 28 residues processed: 343 average time/residue: 0.1655 time to fit residues: 85.4785 Evaluate side-chains 328 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 241 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 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 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 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 241 VAL Chi-restraints excluded: chain D residue 402 SER 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: 2.9990 chunk 130 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 HIS B 745 HIS C 745 HIS D 745 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.145549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.108271 restraints weight = 24161.170| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.85 r_work: 0.3056 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21612 Z= 0.135 Angle : 0.564 9.898 29059 Z= 0.280 Chirality : 0.040 0.265 3224 Planarity : 0.003 0.038 3536 Dihedral : 13.513 105.118 3520 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.57 % Allowed : 19.81 % Favored : 77.62 % 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: -0.60 (0.17), residues: 2472 helix: 1.08 (0.13), residues: 1608 sheet: -2.26 (0.50), residues: 84 loop : -3.48 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.023 0.002 TYR C 260 PHE 0.014 0.001 PHE D 193 TRP 0.020 0.002 TRP B 380 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00309 (21612) covalent geometry : angle 0.56430 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.04473 ( 1072) hydrogen bonds : angle 4.17596 ( 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 372 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 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: 0.7690 (tpp) cc_final: 0.7479 (tpp) REVERT: A 160 HIS cc_start: 0.7366 (t-90) cc_final: 0.6899 (t-90) REVERT: A 174 LYS cc_start: 0.8783 (tttt) cc_final: 0.8471 (tttm) REVERT: A 211 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8270 (mp0) REVERT: A 229 ASP cc_start: 0.7699 (m-30) cc_final: 0.7396 (m-30) REVERT: A 327 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.6873 (tpt170) REVERT: A 677 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8592 (mtp) REVERT: A 687 GLU cc_start: 0.8749 (pp20) cc_final: 0.8412 (pp20) REVERT: A 704 GLU cc_start: 0.7563 (tt0) cc_final: 0.7239 (tt0) REVERT: A 714 ARG cc_start: 0.7615 (ttt-90) cc_final: 0.7016 (ttm170) REVERT: B 122 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6577 (mtp180) REVERT: B 138 LEU cc_start: 0.8203 (mt) cc_final: 0.7965 (mt) REVERT: B 159 MET cc_start: 0.7687 (tpp) cc_final: 0.7473 (tpp) REVERT: B 160 HIS cc_start: 0.7373 (t-90) cc_final: 0.6901 (t-90) REVERT: B 174 LYS cc_start: 0.8774 (tttt) cc_final: 0.8459 (tttm) REVERT: B 211 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8287 (mp0) REVERT: B 229 ASP cc_start: 0.7717 (m-30) cc_final: 0.7407 (m-30) REVERT: B 276 GLU cc_start: 0.7805 (pm20) cc_final: 0.7564 (pm20) REVERT: B 327 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.6857 (tpt170) REVERT: B 677 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8588 (mtp) REVERT: B 687 GLU cc_start: 0.8740 (pp20) cc_final: 0.8409 (pp20) REVERT: B 704 GLU cc_start: 0.7573 (tt0) cc_final: 0.7252 (tt0) REVERT: B 714 ARG cc_start: 0.7624 (ttt-90) cc_final: 0.7022 (ttm170) REVERT: C 122 ARG cc_start: 0.7578 (mtt180) cc_final: 0.6587 (mtp180) REVERT: C 138 LEU cc_start: 0.8205 (mt) cc_final: 0.7967 (mt) REVERT: C 159 MET cc_start: 0.7706 (tpp) cc_final: 0.7493 (tpp) REVERT: C 160 HIS cc_start: 0.7369 (t-90) cc_final: 0.6895 (t-90) REVERT: C 174 LYS cc_start: 0.8789 (tttt) cc_final: 0.8473 (tttm) REVERT: C 211 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8287 (mp0) REVERT: C 229 ASP cc_start: 0.7693 (m-30) cc_final: 0.7386 (m-30) REVERT: C 327 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.6871 (tpt170) REVERT: C 677 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8595 (mtp) REVERT: C 687 GLU cc_start: 0.8752 (pp20) cc_final: 0.8423 (pp20) REVERT: C 704 GLU cc_start: 0.7566 (tt0) cc_final: 0.7238 (tt0) REVERT: C 714 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7042 (ttm170) REVERT: D 122 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6586 (mtp180) REVERT: D 138 LEU cc_start: 0.8204 (mt) cc_final: 0.7966 (mt) REVERT: D 159 MET cc_start: 0.7697 (tpp) cc_final: 0.7485 (tpp) REVERT: D 160 HIS cc_start: 0.7366 (t-90) cc_final: 0.6896 (t-90) REVERT: D 174 LYS cc_start: 0.8770 (tttt) cc_final: 0.8452 (tttm) REVERT: D 211 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8283 (mp0) REVERT: D 229 ASP cc_start: 0.7694 (m-30) cc_final: 0.7392 (m-30) REVERT: D 327 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.6866 (tpt170) REVERT: D 677 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8598 (mtp) REVERT: D 687 GLU cc_start: 0.8749 (pp20) cc_final: 0.8417 (pp20) REVERT: D 704 GLU cc_start: 0.7567 (tt0) cc_final: 0.7243 (tt0) REVERT: D 714 ARG cc_start: 0.7625 (ttt-90) cc_final: 0.7019 (ttm170) outliers start: 57 outliers final: 37 residues processed: 356 average time/residue: 0.1731 time to fit residues: 91.4602 Evaluate side-chains 344 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 303 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 684 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 373 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 684 VAL Chi-restraints excluded: chain B residue 730 LEU 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 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 684 VAL Chi-restraints excluded: chain C residue 730 LEU 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 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 684 VAL 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: 1.9990 chunk 201 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 29 optimal weight: 0.0570 chunk 64 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 ASN D 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.145207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.108410 restraints weight = 23959.627| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.83 r_work: 0.2937 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21612 Z= 0.139 Angle : 0.568 10.022 29059 Z= 0.283 Chirality : 0.040 0.241 3224 Planarity : 0.004 0.063 3536 Dihedral : 13.395 103.232 3520 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.39 % Allowed : 20.58 % Favored : 77.03 % 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: -0.54 (0.17), residues: 2472 helix: 1.08 (0.13), residues: 1636 sheet: -2.08 (0.50), residues: 84 loop : -3.53 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.021 0.001 TYR A 260 PHE 0.024 0.001 PHE C 506 TRP 0.017 0.002 TRP B 380 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00321 (21612) covalent geometry : angle 0.56800 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.04499 ( 1072) hydrogen bonds : angle 4.14651 ( 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 358 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 0.503 Fit side-chains REVERT: A 159 MET cc_start: 0.7585 (tpp) cc_final: 0.7272 (ttt) REVERT: A 160 HIS cc_start: 0.7317 (t-90) cc_final: 0.6854 (t-90) REVERT: A 174 LYS cc_start: 0.8716 (tttt) cc_final: 0.8296 (tttm) REVERT: A 177 LEU cc_start: 0.8456 (mt) cc_final: 0.8188 (mp) REVERT: A 179 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6511 (tp) REVERT: A 202 ARG cc_start: 0.8828 (mtp-110) cc_final: 0.8551 (mtp85) REVERT: A 211 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8306 (mp0) REVERT: A 229 ASP cc_start: 0.7635 (m-30) cc_final: 0.7331 (m-30) REVERT: A 327 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.6881 (tpt170) REVERT: A 488 MET cc_start: 0.7433 (ttp) cc_final: 0.5456 (mmt) REVERT: A 677 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8568 (mtp) REVERT: A 687 GLU cc_start: 0.8716 (pp20) cc_final: 0.8365 (pp20) REVERT: A 704 GLU cc_start: 0.7543 (tt0) cc_final: 0.7215 (tt0) REVERT: A 714 ARG cc_start: 0.7606 (ttt-90) cc_final: 0.7001 (ttm170) REVERT: B 122 ARG cc_start: 0.7560 (mtt180) cc_final: 0.6563 (mtp180) REVERT: B 138 LEU cc_start: 0.8183 (mt) cc_final: 0.7944 (mt) REVERT: B 159 MET cc_start: 0.7610 (tpp) cc_final: 0.7285 (ttt) REVERT: B 160 HIS cc_start: 0.7321 (t-90) cc_final: 0.6857 (t-90) REVERT: B 174 LYS cc_start: 0.8693 (tttt) cc_final: 0.8260 (tttm) REVERT: B 177 LEU cc_start: 0.8448 (mt) cc_final: 0.8181 (mp) REVERT: B 179 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6517 (tp) REVERT: B 202 ARG cc_start: 0.8838 (mtp-110) cc_final: 0.8561 (mtp85) REVERT: B 211 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8322 (mp0) REVERT: B 229 ASP cc_start: 0.7659 (m-30) cc_final: 0.7351 (m-30) REVERT: B 276 GLU cc_start: 0.7776 (pm20) cc_final: 0.7547 (pm20) REVERT: B 327 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.6880 (tpt170) REVERT: B 488 MET cc_start: 0.7450 (ttp) cc_final: 0.5469 (mmt) REVERT: B 677 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8568 (mtp) REVERT: B 687 GLU cc_start: 0.8706 (pp20) cc_final: 0.8354 (pp20) REVERT: B 704 GLU cc_start: 0.7557 (tt0) cc_final: 0.7228 (tt0) REVERT: B 714 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.6998 (ttm170) REVERT: C 122 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6564 (mtp180) REVERT: C 138 LEU cc_start: 0.8177 (mt) cc_final: 0.7939 (mt) REVERT: C 159 MET cc_start: 0.7587 (tpp) cc_final: 0.7279 (ttt) REVERT: C 160 HIS cc_start: 0.7313 (t-90) cc_final: 0.6849 (t-90) REVERT: C 174 LYS cc_start: 0.8684 (tttt) cc_final: 0.8253 (tttm) REVERT: C 177 LEU cc_start: 0.8439 (mt) cc_final: 0.8172 (mp) REVERT: C 179 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6528 (tp) REVERT: C 202 ARG cc_start: 0.8840 (mtp-110) cc_final: 0.8569 (mtp85) REVERT: C 211 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8330 (mp0) REVERT: C 229 ASP cc_start: 0.7625 (m-30) cc_final: 0.7322 (m-30) REVERT: C 327 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.6879 (tpt170) REVERT: C 488 MET cc_start: 0.7449 (ttp) cc_final: 0.5468 (mmt) REVERT: C 677 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8574 (mtp) REVERT: C 687 GLU cc_start: 0.8718 (pp20) cc_final: 0.8371 (pp20) REVERT: C 704 GLU cc_start: 0.7544 (tt0) cc_final: 0.7210 (tt0) REVERT: C 714 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7018 (ttm170) REVERT: D 122 ARG cc_start: 0.7563 (mtt180) cc_final: 0.6569 (mtp180) REVERT: D 138 LEU cc_start: 0.8179 (mt) cc_final: 0.7938 (mt) REVERT: D 159 MET cc_start: 0.7597 (tpp) cc_final: 0.7278 (ttt) REVERT: D 160 HIS cc_start: 0.7316 (t-90) cc_final: 0.6851 (t-90) REVERT: D 174 LYS cc_start: 0.8685 (tttt) cc_final: 0.8252 (tttm) REVERT: D 177 LEU cc_start: 0.8424 (mt) cc_final: 0.8155 (mp) REVERT: D 179 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6519 (tp) REVERT: D 202 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8566 (mtp85) REVERT: D 211 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8316 (mp0) REVERT: D 229 ASP cc_start: 0.7633 (m-30) cc_final: 0.7324 (m-30) REVERT: D 327 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.6881 (tpt170) REVERT: D 488 MET cc_start: 0.7453 (ttp) cc_final: 0.5468 (mmt) REVERT: D 677 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: D 687 GLU cc_start: 0.8722 (pp20) cc_final: 0.8373 (pp20) REVERT: D 704 GLU cc_start: 0.7560 (tt0) cc_final: 0.7230 (tt0) REVERT: D 714 ARG cc_start: 0.7601 (ttt-90) cc_final: 0.6991 (ttm170) outliers start: 53 outliers final: 34 residues processed: 339 average time/residue: 0.1668 time to fit residues: 84.5636 Evaluate side-chains 341 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 399 THR Chi-restraints excluded: chain A residue 402 SER 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 179 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 402 SER 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 179 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 SER 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 179 ILE Chi-restraints excluded: chain D residue 241 VAL 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: 0.9990 chunk 67 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 ASN D 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.146800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.109999 restraints weight = 24085.608| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.85 r_work: 0.2964 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21612 Z= 0.119 Angle : 0.556 9.278 29059 Z= 0.276 Chirality : 0.039 0.225 3224 Planarity : 0.003 0.052 3536 Dihedral : 13.172 100.692 3520 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.53 % Allowed : 21.34 % Favored : 76.13 % 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: -0.40 (0.17), residues: 2472 helix: 1.25 (0.13), residues: 1612 sheet: -2.08 (0.50), residues: 84 loop : -3.47 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.018 0.001 TYR C 260 PHE 0.012 0.001 PHE A 193 TRP 0.018 0.002 TRP B 380 HIS 0.004 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00266 (21612) covalent geometry : angle 0.55656 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.04145 ( 1072) hydrogen bonds : angle 4.02083 ( 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 354 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.7598 (tpp) cc_final: 0.7287 (ttt) REVERT: A 160 HIS cc_start: 0.7328 (t-90) cc_final: 0.6870 (t-90) REVERT: A 174 LYS cc_start: 0.8711 (tttt) cc_final: 0.8316 (tttm) REVERT: A 177 LEU cc_start: 0.8450 (mt) cc_final: 0.8173 (mp) REVERT: A 179 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6441 (tp) REVERT: A 185 GLU cc_start: 0.7693 (mp0) cc_final: 0.7194 (mp0) REVERT: A 202 ARG cc_start: 0.8810 (mtp-110) cc_final: 0.8429 (mtp85) REVERT: A 211 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8319 (mp0) REVERT: A 229 ASP cc_start: 0.7604 (m-30) cc_final: 0.7330 (m-30) REVERT: A 327 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.6882 (tpt170) REVERT: A 677 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8574 (mtp) REVERT: A 687 GLU cc_start: 0.8723 (pp20) cc_final: 0.8396 (pp20) REVERT: A 704 GLU cc_start: 0.7502 (tt0) cc_final: 0.7166 (tt0) REVERT: A 714 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.6994 (ttm170) REVERT: B 122 ARG cc_start: 0.7572 (mtt180) cc_final: 0.6577 (mtp180) REVERT: B 138 LEU cc_start: 0.8194 (mt) cc_final: 0.7927 (mt) REVERT: B 159 MET cc_start: 0.7620 (tpp) cc_final: 0.7298 (ttt) REVERT: B 160 HIS cc_start: 0.7328 (t-90) cc_final: 0.6867 (t-90) REVERT: B 174 LYS cc_start: 0.8698 (tttt) cc_final: 0.8304 (tttm) REVERT: B 177 LEU cc_start: 0.8447 (mt) cc_final: 0.8168 (mp) REVERT: B 179 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6445 (tp) REVERT: B 185 GLU cc_start: 0.7721 (mp0) cc_final: 0.7213 (mp0) REVERT: B 202 ARG cc_start: 0.8819 (mtp-110) cc_final: 0.8435 (mtp85) REVERT: B 211 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8338 (mp0) REVERT: B 229 ASP cc_start: 0.7639 (m-30) cc_final: 0.7357 (m-30) REVERT: B 276 GLU cc_start: 0.7750 (pm20) cc_final: 0.7479 (pm20) REVERT: B 327 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.6876 (tpt170) REVERT: B 677 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: B 687 GLU cc_start: 0.8737 (pp20) cc_final: 0.8412 (pp20) REVERT: B 704 GLU cc_start: 0.7512 (tt0) cc_final: 0.7178 (tt0) REVERT: B 714 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.6995 (ttm170) REVERT: C 122 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6575 (mtp180) REVERT: C 138 LEU cc_start: 0.8187 (mt) cc_final: 0.7922 (mt) REVERT: C 159 MET cc_start: 0.7609 (tpp) cc_final: 0.7296 (ttt) REVERT: C 160 HIS cc_start: 0.7321 (t-90) cc_final: 0.6860 (t-90) REVERT: C 174 LYS cc_start: 0.8699 (tttt) cc_final: 0.8301 (tttm) REVERT: C 177 LEU cc_start: 0.8433 (mt) cc_final: 0.8157 (mp) REVERT: C 179 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6457 (tp) REVERT: C 185 GLU cc_start: 0.7716 (mp0) cc_final: 0.7209 (mp0) REVERT: C 202 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8442 (mtp85) REVERT: C 211 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8355 (mp0) REVERT: C 229 ASP cc_start: 0.7591 (m-30) cc_final: 0.7310 (m-30) REVERT: C 327 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.6870 (tpt170) REVERT: C 677 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8576 (mtp) REVERT: C 687 GLU cc_start: 0.8739 (pp20) cc_final: 0.8418 (pp20) REVERT: C 704 GLU cc_start: 0.7488 (tt0) cc_final: 0.7152 (tt0) REVERT: C 714 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.7029 (ttm170) REVERT: D 122 ARG cc_start: 0.7569 (mtt180) cc_final: 0.6577 (mtp180) REVERT: D 138 LEU cc_start: 0.8185 (mt) cc_final: 0.7921 (mt) REVERT: D 159 MET cc_start: 0.7612 (tpp) cc_final: 0.7296 (ttt) REVERT: D 160 HIS cc_start: 0.7321 (t-90) cc_final: 0.6860 (t-90) REVERT: D 174 LYS cc_start: 0.8697 (tttt) cc_final: 0.8304 (tttm) REVERT: D 177 LEU cc_start: 0.8429 (mt) cc_final: 0.8151 (mp) REVERT: D 179 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6445 (tp) REVERT: D 185 GLU cc_start: 0.7704 (mp0) cc_final: 0.7190 (mp0) REVERT: D 202 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8436 (mtp85) REVERT: D 211 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8341 (mp0) REVERT: D 229 ASP cc_start: 0.7596 (m-30) cc_final: 0.7319 (m-30) REVERT: D 327 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.6875 (tpt170) REVERT: D 677 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8580 (mtp) REVERT: D 687 GLU cc_start: 0.8736 (pp20) cc_final: 0.8413 (pp20) REVERT: D 704 GLU cc_start: 0.7506 (tt0) cc_final: 0.7171 (tt0) REVERT: D 714 ARG cc_start: 0.7628 (ttt-90) cc_final: 0.7007 (ttm170) outliers start: 56 outliers final: 38 residues processed: 335 average time/residue: 0.1647 time to fit residues: 82.6509 Evaluate side-chains 334 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 572 MET 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 241 VAL Chi-restraints excluded: chain B residue 373 LEU 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 179 ILE Chi-restraints excluded: chain C residue 241 VAL 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 179 ILE Chi-restraints excluded: chain D residue 241 VAL 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: 0.0980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 0.0770 chunk 130 optimal weight: 0.3980 chunk 138 optimal weight: 0.0060 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 63 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 overall best weight: 0.1252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 745 HIS B 251 ASN B 745 HIS C 251 ASN C 412 ASN C 745 HIS D 251 ASN D 412 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.152937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.118043 restraints weight = 23969.573| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.75 r_work: 0.3071 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3177 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= 0.094 Angle : 0.503 8.451 29059 Z= 0.253 Chirality : 0.037 0.216 3224 Planarity : 0.003 0.046 3536 Dihedral : 12.456 95.219 3520 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.12 % Allowed : 21.21 % Favored : 76.67 % 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: -0.19 (0.17), residues: 2472 helix: 1.38 (0.13), residues: 1628 sheet: -1.92 (0.51), residues: 84 loop : -3.45 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 136 TYR 0.011 0.001 TYR A 564 PHE 0.013 0.001 PHE A 193 TRP 0.011 0.001 TRP D 692 HIS 0.004 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00188 (21612) covalent geometry : angle 0.50318 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.03221 ( 1072) hydrogen bonds : angle 3.72210 ( 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 390 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 343 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 160 HIS cc_start: 0.7244 (t-90) cc_final: 0.6844 (t-90) REVERT: A 174 LYS cc_start: 0.8605 (tttt) cc_final: 0.8371 (tttp) REVERT: A 202 ARG cc_start: 0.8730 (mtp-110) cc_final: 0.8326 (mtp85) REVERT: A 211 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8104 (mp0) REVERT: A 248 VAL cc_start: 0.7920 (p) cc_final: 0.7496 (t) REVERT: A 327 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.6794 (tpt170) REVERT: A 488 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6292 (ttm) REVERT: A 643 ASN cc_start: 0.7523 (m-40) cc_final: 0.6519 (p0) REVERT: A 677 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8500 (mtp) REVERT: A 687 GLU cc_start: 0.8589 (pp20) cc_final: 0.8363 (pp20) REVERT: A 704 GLU cc_start: 0.7288 (tt0) cc_final: 0.6949 (tt0) REVERT: A 714 ARG cc_start: 0.7628 (ttt-90) cc_final: 0.6955 (ttm110) REVERT: A 719 GLU cc_start: 0.8067 (pm20) cc_final: 0.7738 (pm20) REVERT: B 122 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6247 (mtp180) REVERT: B 138 LEU cc_start: 0.8168 (mt) cc_final: 0.7961 (mt) REVERT: B 160 HIS cc_start: 0.7244 (t-90) cc_final: 0.6836 (t-90) REVERT: B 174 LYS cc_start: 0.8589 (tttt) cc_final: 0.8352 (tttp) REVERT: B 202 ARG cc_start: 0.8730 (mtp-110) cc_final: 0.8319 (mtp85) REVERT: B 211 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8099 (mp0) REVERT: B 248 VAL cc_start: 0.7918 (p) cc_final: 0.7496 (t) REVERT: B 276 GLU cc_start: 0.7736 (pm20) cc_final: 0.7468 (pm20) REVERT: B 327 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.6836 (tpt170) REVERT: B 488 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6302 (ttm) REVERT: B 643 ASN cc_start: 0.7528 (m-40) cc_final: 0.6525 (p0) REVERT: B 677 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8486 (mtp) REVERT: B 687 GLU cc_start: 0.8588 (pp20) cc_final: 0.8366 (pp20) REVERT: B 704 GLU cc_start: 0.7293 (tt0) cc_final: 0.6956 (tt0) REVERT: B 714 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.6967 (ttm110) REVERT: B 719 GLU cc_start: 0.8073 (pm20) cc_final: 0.7746 (pm20) REVERT: C 122 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6239 (mtp180) REVERT: C 138 LEU cc_start: 0.8165 (mt) cc_final: 0.7960 (mt) REVERT: C 160 HIS cc_start: 0.7232 (t-90) cc_final: 0.6827 (t-90) REVERT: C 174 LYS cc_start: 0.8585 (tttt) cc_final: 0.8348 (tttp) REVERT: C 202 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8333 (mtp85) REVERT: C 211 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8115 (mp0) REVERT: C 248 VAL cc_start: 0.7901 (p) cc_final: 0.7502 (t) REVERT: C 327 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.6789 (tpt170) REVERT: C 488 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6294 (ttm) REVERT: C 643 ASN cc_start: 0.7531 (m-40) cc_final: 0.6526 (p0) REVERT: C 677 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: C 687 GLU cc_start: 0.8612 (pp20) cc_final: 0.8387 (pp20) REVERT: C 704 GLU cc_start: 0.7277 (tt0) cc_final: 0.6942 (tt0) REVERT: C 714 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.6982 (ttm110) REVERT: C 719 GLU cc_start: 0.8070 (pm20) cc_final: 0.7746 (pm20) REVERT: D 122 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6247 (mtp180) REVERT: D 138 LEU cc_start: 0.8166 (mt) cc_final: 0.7959 (mt) REVERT: D 160 HIS cc_start: 0.7228 (t-90) cc_final: 0.6826 (t-90) REVERT: D 174 LYS cc_start: 0.8592 (tttt) cc_final: 0.8350 (tttp) REVERT: D 202 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8335 (mtp85) REVERT: D 211 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8087 (mp0) REVERT: D 248 VAL cc_start: 0.7898 (p) cc_final: 0.7490 (t) REVERT: D 327 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.6794 (tpt170) REVERT: D 488 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6320 (ttm) REVERT: D 643 ASN cc_start: 0.7523 (m-40) cc_final: 0.6507 (p0) REVERT: D 677 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8602 (mtp) REVERT: D 687 GLU cc_start: 0.8602 (pp20) cc_final: 0.8375 (pp20) REVERT: D 704 GLU cc_start: 0.7293 (tt0) cc_final: 0.6953 (tt0) REVERT: D 714 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.6965 (ttm110) REVERT: D 719 GLU cc_start: 0.8035 (pm20) cc_final: 0.7705 (pm20) outliers start: 47 outliers final: 23 residues processed: 366 average time/residue: 0.1639 time to fit residues: 90.4393 Evaluate side-chains 355 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 324 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 488 MET 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 B residue 241 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 488 MET 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 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 488 MET Chi-restraints excluded: chain C residue 508 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 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 488 MET Chi-restraints excluded: chain D residue 508 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 171 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 412 ASN B 256 HIS B 412 ASN C 256 HIS C 412 ASN D 256 HIS D 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.147974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.112605 restraints weight = 24041.337| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.76 r_work: 0.3084 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21612 Z= 0.122 Angle : 0.546 8.788 29059 Z= 0.269 Chirality : 0.039 0.158 3224 Planarity : 0.003 0.046 3536 Dihedral : 12.446 98.465 3520 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.99 % Allowed : 21.66 % Favored : 76.35 % 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: -0.16 (0.17), residues: 2472 helix: 1.38 (0.13), residues: 1636 sheet: -1.86 (0.52), residues: 84 loop : -3.45 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 729 TYR 0.015 0.001 TYR B 260 PHE 0.013 0.001 PHE A 316 TRP 0.014 0.001 TRP D 380 HIS 0.004 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00281 (21612) covalent geometry : angle 0.54647 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.04016 ( 1072) hydrogen bonds : angle 3.85509 ( 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 336 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.8000 (mt) cc_final: 0.7733 (mt) REVERT: A 160 HIS cc_start: 0.7310 (t-90) cc_final: 0.6931 (t-90) REVERT: A 211 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8308 (mp0) REVERT: A 251 ASN cc_start: 0.8798 (t0) cc_final: 0.8335 (t0) REVERT: A 327 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.6850 (tpt170) REVERT: A 488 MET cc_start: 0.6844 (ttp) cc_final: 0.6563 (ttm) REVERT: A 677 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8601 (mtp) REVERT: A 687 GLU cc_start: 0.8703 (pp20) cc_final: 0.8445 (pp20) REVERT: A 704 GLU cc_start: 0.7288 (tt0) cc_final: 0.6971 (tt0) REVERT: A 714 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.6960 (ttm110) REVERT: B 138 LEU cc_start: 0.8255 (mt) cc_final: 0.7988 (mt) REVERT: B 160 HIS cc_start: 0.7304 (t-90) cc_final: 0.6923 (t-90) REVERT: B 174 LYS cc_start: 0.8719 (tttt) cc_final: 0.8495 (tttp) REVERT: B 211 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8304 (mp0) REVERT: B 327 ARG cc_start: 0.8056 (mmm-85) cc_final: 0.6844 (tpt170) REVERT: B 488 MET cc_start: 0.6851 (ttp) cc_final: 0.6565 (ttm) REVERT: B 677 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8595 (mtp) REVERT: B 687 GLU cc_start: 0.8713 (pp20) cc_final: 0.8455 (pp20) REVERT: B 704 GLU cc_start: 0.7297 (tt0) cc_final: 0.6981 (tt0) REVERT: B 714 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.6956 (ttm110) REVERT: C 138 LEU cc_start: 0.8260 (mt) cc_final: 0.7992 (mt) REVERT: C 160 HIS cc_start: 0.7316 (t-90) cc_final: 0.6933 (t-90) REVERT: C 174 LYS cc_start: 0.8727 (tttt) cc_final: 0.8504 (tttp) REVERT: C 211 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8311 (mp0) REVERT: C 327 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.6847 (tpt170) REVERT: C 488 MET cc_start: 0.6840 (ttp) cc_final: 0.6554 (ttm) REVERT: C 677 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8600 (mtp) REVERT: C 687 GLU cc_start: 0.8722 (pp20) cc_final: 0.8467 (pp20) REVERT: C 704 GLU cc_start: 0.7280 (tt0) cc_final: 0.6960 (tt0) REVERT: C 714 ARG cc_start: 0.7604 (ttt-90) cc_final: 0.6967 (ttm110) REVERT: D 138 LEU cc_start: 0.8267 (mt) cc_final: 0.8001 (mt) REVERT: D 160 HIS cc_start: 0.7320 (t-90) cc_final: 0.6940 (t-90) REVERT: D 174 LYS cc_start: 0.8711 (tttt) cc_final: 0.8490 (tttp) REVERT: D 211 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8307 (mp0) REVERT: D 327 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.6852 (tpt170) REVERT: D 488 MET cc_start: 0.6847 (ttp) cc_final: 0.6566 (ttm) REVERT: D 677 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8606 (mtp) REVERT: D 687 GLU cc_start: 0.8711 (pp20) cc_final: 0.8454 (pp20) REVERT: D 704 GLU cc_start: 0.7301 (tt0) cc_final: 0.6982 (tt0) REVERT: D 714 ARG cc_start: 0.7584 (ttt-90) cc_final: 0.6955 (ttm110) outliers start: 44 outliers final: 27 residues processed: 317 average time/residue: 0.1688 time to fit residues: 79.4874 Evaluate side-chains 320 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 373 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 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 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 572 MET 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 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 572 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 103 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 78 optimal weight: 0.0270 chunk 89 optimal weight: 0.0020 chunk 120 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 412 ASN B 256 HIS B 412 ASN C 256 HIS C 412 ASN D 256 HIS D 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.150562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.115475 restraints weight = 24143.969| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.75 r_work: 0.3040 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21612 Z= 0.097 Angle : 0.522 8.723 29059 Z= 0.258 Chirality : 0.038 0.156 3224 Planarity : 0.003 0.044 3536 Dihedral : 12.213 97.970 3520 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.76 % Allowed : 21.75 % Favored : 76.49 % 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: -0.07 (0.17), residues: 2472 helix: 1.47 (0.13), residues: 1628 sheet: -1.74 (0.53), residues: 84 loop : -3.42 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.021 0.001 TYR C 260 PHE 0.012 0.001 PHE A 193 TRP 0.013 0.001 TRP C 380 HIS 0.004 0.001 HIS C 745 Details of bonding type rmsd covalent geometry : bond 0.00204 (21612) covalent geometry : angle 0.52232 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.03502 ( 1072) hydrogen bonds : angle 3.75416 ( 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 337 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 160 HIS cc_start: 0.7523 (t-90) cc_final: 0.7107 (t70) REVERT: A 211 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8256 (mp0) REVERT: A 251 ASN cc_start: 0.8641 (t0) cc_final: 0.8417 (t0) REVERT: A 327 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.6781 (tpt170) REVERT: A 334 GLU cc_start: 0.8986 (tt0) cc_final: 0.8766 (tt0) REVERT: A 488 MET cc_start: 0.6893 (ttp) cc_final: 0.6680 (ttm) REVERT: A 677 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8584 (mtp) REVERT: A 687 GLU cc_start: 0.8641 (pp20) cc_final: 0.8392 (pp20) REVERT: A 704 GLU cc_start: 0.7314 (tt0) cc_final: 0.6987 (tt0) REVERT: A 714 ARG cc_start: 0.7565 (ttt-90) cc_final: 0.6933 (ttm110) REVERT: A 719 GLU cc_start: 0.8090 (pm20) cc_final: 0.7881 (pm20) REVERT: B 138 LEU cc_start: 0.8226 (mt) cc_final: 0.7988 (mt) REVERT: B 160 HIS cc_start: 0.7511 (t-90) cc_final: 0.7087 (t70) REVERT: B 211 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8246 (mp0) REVERT: B 251 ASN cc_start: 0.8609 (t0) cc_final: 0.8393 (t0) REVERT: B 327 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.6777 (tpt170) REVERT: B 334 GLU cc_start: 0.8955 (tt0) cc_final: 0.8720 (tt0) REVERT: B 488 MET cc_start: 0.6893 (ttp) cc_final: 0.6677 (ttm) REVERT: B 677 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8580 (mtp) REVERT: B 687 GLU cc_start: 0.8632 (pp20) cc_final: 0.8385 (pp20) REVERT: B 704 GLU cc_start: 0.7332 (tt0) cc_final: 0.7004 (tt0) REVERT: B 714 ARG cc_start: 0.7576 (ttt-90) cc_final: 0.6940 (ttm110) REVERT: B 719 GLU cc_start: 0.8091 (pm20) cc_final: 0.7890 (pm20) REVERT: C 138 LEU cc_start: 0.8232 (mt) cc_final: 0.7995 (mt) REVERT: C 160 HIS cc_start: 0.7514 (t-90) cc_final: 0.7090 (t70) REVERT: C 211 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8260 (mp0) REVERT: C 251 ASN cc_start: 0.8630 (t0) cc_final: 0.8401 (t0) REVERT: C 327 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.6772 (tpt170) REVERT: C 334 GLU cc_start: 0.8950 (tt0) cc_final: 0.8732 (tt0) REVERT: C 488 MET cc_start: 0.6893 (ttp) cc_final: 0.6675 (ttm) REVERT: C 677 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8584 (mtp) REVERT: C 687 GLU cc_start: 0.8656 (pp20) cc_final: 0.8410 (pp20) REVERT: C 704 GLU cc_start: 0.7308 (tt0) cc_final: 0.6976 (tt0) REVERT: C 714 ARG cc_start: 0.7584 (ttt-90) cc_final: 0.6946 (ttm110) REVERT: C 719 GLU cc_start: 0.8088 (pm20) cc_final: 0.7875 (pm20) REVERT: D 138 LEU cc_start: 0.8223 (mt) cc_final: 0.7988 (mt) REVERT: D 160 HIS cc_start: 0.7519 (t-90) cc_final: 0.7093 (t70) REVERT: D 211 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8247 (mp0) REVERT: D 251 ASN cc_start: 0.8623 (t0) cc_final: 0.8398 (t0) REVERT: D 327 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.6779 (tpt170) REVERT: D 334 GLU cc_start: 0.8970 (tt0) cc_final: 0.8754 (tt0) REVERT: D 488 MET cc_start: 0.6906 (ttp) cc_final: 0.6694 (ttm) REVERT: D 677 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: D 687 GLU cc_start: 0.8638 (pp20) cc_final: 0.8384 (pp20) REVERT: D 704 GLU cc_start: 0.7338 (tt0) cc_final: 0.7010 (tt0) REVERT: D 714 ARG cc_start: 0.7574 (ttt-90) cc_final: 0.6938 (ttm110) REVERT: D 719 GLU cc_start: 0.8087 (pm20) cc_final: 0.7878 (pm20) outliers start: 39 outliers final: 27 residues processed: 323 average time/residue: 0.1718 time to fit residues: 82.4171 Evaluate side-chains 319 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 373 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 508 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 402 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 572 MET 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 402 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 572 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 412 ASN B 256 HIS B 412 ASN C 256 HIS C 412 ASN D 256 HIS D 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.146016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.110411 restraints weight = 24199.038| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.77 r_work: 0.2970 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21612 Z= 0.146 Angle : 0.568 9.673 29059 Z= 0.282 Chirality : 0.040 0.145 3224 Planarity : 0.004 0.045 3536 Dihedral : 12.463 100.667 3520 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 1.94 % Allowed : 22.11 % Favored : 75.95 % 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: -0.18 (0.17), residues: 2472 helix: 1.34 (0.13), residues: 1652 sheet: -1.84 (0.52), residues: 84 loop : -3.47 (0.19), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 202 TYR 0.026 0.002 TYR D 260 PHE 0.015 0.001 PHE D 316 TRP 0.015 0.002 TRP D 380 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00343 (21612) covalent geometry : angle 0.56828 (29048) SS BOND : angle 0.00000 ( 11) hydrogen bonds : bond 0.04454 ( 1072) hydrogen bonds : angle 3.92005 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5451.74 seconds wall clock time: 93 minutes 46.54 seconds (5626.54 seconds total)