Starting phenix.real_space_refine on Mon Apr 6 08:49:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3i_47484/04_2026/9e3i_47484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3i_47484/04_2026/9e3i_47484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3i_47484/04_2026/9e3i_47484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3i_47484/04_2026/9e3i_47484.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3i_47484/04_2026/9e3i_47484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3i_47484/04_2026/9e3i_47484.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10653 2.51 5 N 2946 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16818 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5578 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 29, 'TRANS': 671} Chain breaks: 5 Chain: "C" Number of atoms: 5578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5578 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 29, 'TRANS': 671} Chain breaks: 5 Chain: "B" Number of atoms: 5578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5578 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 29, 'TRANS': 671} Chain breaks: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.10, per 1000 atoms: 0.18 Number of scatterers: 16818 At special positions: 0 Unit cell: (124.08, 113.52, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3129 8.00 N 2946 7.00 C 10653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG A1002 " - " ASN A 398 " " NAG B1001 " - " ASN B 141 " " NAG B1002 " - " ASN B 398 " " NAG C1001 " - " ASN C 141 " " NAG C1002 " - " ASN C 398 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 502.3 milliseconds 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 36 sheets defined 36.7% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.720A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.779A pdb=" N VAL A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.973A pdb=" N ASP A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 510 through 546 removed outlier: 4.547A pdb=" N HIS A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 701 through 724 Processing helix chain 'A' and resid 726 through 739 removed outlier: 4.259A pdb=" N ALA A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 773 removed outlier: 3.696A pdb=" N ASN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 removed outlier: 3.782A pdb=" N SER A 803 " --> pdb=" O MET A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 837 through 859 removed outlier: 3.806A pdb=" N THR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.965A pdb=" N VAL C 407 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.873A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 467 Processing helix chain 'C' and resid 510 through 546 removed outlier: 4.467A pdb=" N HIS C 516 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 701 through 724 Processing helix chain 'C' and resid 726 through 739 removed outlier: 4.263A pdb=" N ALA C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 773 removed outlier: 3.729A pdb=" N ASN C 773 " --> pdb=" O SER C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 803 removed outlier: 3.808A pdb=" N SER C 803 " --> pdb=" O MET C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 810 Processing helix chain 'C' and resid 837 through 859 removed outlier: 3.803A pdb=" N ARG C 858 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 859 " --> pdb=" O ALA C 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 260 through 266 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.065A pdb=" N VAL B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.590A pdb=" N ASP B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 510 through 546 removed outlier: 4.382A pdb=" N HIS B 516 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 701 through 724 Processing helix chain 'B' and resid 726 through 739 removed outlier: 4.259A pdb=" N ALA B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 773 removed outlier: 3.707A pdb=" N ASN B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 803 removed outlier: 3.779A pdb=" N SER B 803 " --> pdb=" O MET B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'B' and resid 837 through 859 removed outlier: 3.742A pdb=" N ARG B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR B 859 " --> pdb=" O ALA B 855 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 3.898A pdb=" N THR C 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.687A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.687A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 3.617A pdb=" N ARG A 245 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG A 342 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP A 323 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 344 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR A 346 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 319 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AB3, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.580A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.265A pdb=" N THR A 665 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AB6, first strand: chain 'C' and resid 559 through 563 removed outlier: 3.920A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.666A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.666A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AC1, first strand: chain 'C' and resid 235 through 236 removed outlier: 3.627A pdb=" N ARG C 245 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG C 342 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP C 323 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU C 344 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN C 321 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR C 346 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE C 319 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AC4, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AC5, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC6, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AC7, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.582A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AC9, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.674A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.674A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 186 through 191 Processing sheet with id=AD3, first strand: chain 'B' and resid 235 through 236 removed outlier: 3.602A pdb=" N ARG B 245 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG B 342 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASP B 323 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 344 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN B 321 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR B 346 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE B 319 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AD5, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AD6, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AD7, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AD8, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AD9, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.584A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2547 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: 3.21 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5568 1.34 - 1.47: 4315 1.47 - 1.59: 7178 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 17211 Sorted by residual: bond pdb=" CA GLY C 565 " pdb=" C GLY C 565 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.22e+00 bond pdb=" N GLY A 565 " pdb=" CA GLY A 565 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.06e+00 bond pdb=" CA GLY A 565 " pdb=" C GLY A 565 " ideal model delta sigma weight residual 1.514 1.529 -0.014 1.41e-02 5.03e+03 1.06e+00 bond pdb=" N TYR C 282 " pdb=" CA TYR C 282 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.41e-02 5.03e+03 1.04e+00 bond pdb=" N TYR B 282 " pdb=" CA TYR B 282 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.41e-02 5.03e+03 1.00e+00 ... (remaining 17206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 22911 1.49 - 2.97: 344 2.97 - 4.46: 66 4.46 - 5.94: 13 5.94 - 7.43: 6 Bond angle restraints: 23340 Sorted by residual: angle pdb=" N PHE C 508 " pdb=" CA PHE C 508 " pdb=" CB PHE C 508 " ideal model delta sigma weight residual 113.15 108.13 5.02 1.63e+00 3.76e-01 9.48e+00 angle pdb=" N TYR C 282 " pdb=" CA TYR C 282 " pdb=" C TYR C 282 " ideal model delta sigma weight residual 109.81 116.48 -6.67 2.21e+00 2.05e-01 9.12e+00 angle pdb=" N TYR A 282 " pdb=" CA TYR A 282 " pdb=" C TYR A 282 " ideal model delta sigma weight residual 109.81 116.43 -6.62 2.21e+00 2.05e-01 8.98e+00 angle pdb=" N TYR B 282 " pdb=" CA TYR B 282 " pdb=" C TYR B 282 " ideal model delta sigma weight residual 109.81 116.43 -6.62 2.21e+00 2.05e-01 8.98e+00 angle pdb=" N THR B 365 " pdb=" CA THR B 365 " pdb=" C THR B 365 " ideal model delta sigma weight residual 111.28 114.38 -3.10 1.09e+00 8.42e-01 8.07e+00 ... (remaining 23335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8873 17.86 - 35.71: 1023 35.71 - 53.57: 324 53.57 - 71.43: 65 71.43 - 89.29: 29 Dihedral angle restraints: 10314 sinusoidal: 4176 harmonic: 6138 Sorted by residual: dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual -86.00 -167.84 81.84 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual -86.00 -167.55 81.55 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual -86.00 -167.54 81.54 1 1.00e+01 1.00e-02 8.19e+01 ... (remaining 10311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2381 0.077 - 0.155: 184 0.155 - 0.232: 0 0.232 - 0.310: 2 0.310 - 0.387: 1 Chirality restraints: 2568 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 141 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2565 not shown) Planarity restraints: 3033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 508 " 0.029 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE C 508 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE C 508 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 508 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 508 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 508 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE C 508 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 508 " -0.009 2.00e-02 2.50e+03 1.13e-02 2.25e+00 pdb=" CG PHE A 508 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 508 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 508 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 508 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 508 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 508 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 508 " -0.010 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE B 508 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 508 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 508 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 508 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 508 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 508 " -0.000 2.00e-02 2.50e+03 ... (remaining 3030 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3414 2.78 - 3.31: 14606 3.31 - 3.84: 27115 3.84 - 4.37: 31648 4.37 - 4.90: 56616 Nonbonded interactions: 133399 Sorted by model distance: nonbonded pdb=" OG SER A 854 " pdb=" OH TYR C 810 " model vdw 2.249 3.040 nonbonded pdb=" OG SER C 854 " pdb=" OH TYR B 810 " model vdw 2.253 3.040 nonbonded pdb=" O SER C 660 " pdb=" OG SER C 660 " model vdw 2.273 3.040 nonbonded pdb=" O SER A 660 " pdb=" OG SER A 660 " model vdw 2.273 3.040 nonbonded pdb=" O SER B 660 " pdb=" OG SER B 660 " model vdw 2.275 3.040 ... (remaining 133394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 9.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.790 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.003 0.026 17232 Z= 0.119 Angle : 0.497 7.431 23388 Z= 0.268 Chirality : 0.041 0.387 2568 Planarity : 0.003 0.030 3027 Dihedral : 17.123 89.286 6321 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.67 % Allowed : 26.12 % Favored : 71.21 % 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: 1.46 (0.19), residues: 2067 helix: 2.84 (0.20), residues: 690 sheet: 0.59 (0.24), residues: 507 loop : -0.32 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 132 TYR 0.012 0.001 TYR A 282 PHE 0.062 0.001 PHE C 508 TRP 0.004 0.001 TRP C 247 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00256 (17211) covalent geometry : angle 0.48882 (23340) SS BOND : bond 0.00285 ( 15) SS BOND : angle 1.35176 ( 30) hydrogen bonds : bond 0.14355 ( 835) hydrogen bonds : angle 6.77220 ( 2547) link_NAG-ASN : bond 0.00556 ( 6) link_NAG-ASN : angle 2.75729 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.6308 (mtm) cc_final: 0.5934 (mtm) REVERT: A 326 TYR cc_start: 0.7168 (m-80) cc_final: 0.6740 (m-80) REVERT: A 664 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 704 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 799 MET cc_start: 0.8225 (mmp) cc_final: 0.7527 (mmm) REVERT: C 138 GLU cc_start: 0.6987 (tp30) cc_final: 0.6060 (tp30) REVERT: C 281 VAL cc_start: 0.7456 (t) cc_final: 0.6867 (t) REVERT: C 326 TYR cc_start: 0.7106 (m-80) cc_final: 0.6581 (m-80) REVERT: C 664 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8591 (mm) REVERT: B 107 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.4766 (pm20) REVERT: B 138 GLU cc_start: 0.6979 (tp30) cc_final: 0.5834 (tp30) REVERT: B 242 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5666 (mmt90) REVERT: B 322 VAL cc_start: 0.7728 (p) cc_final: 0.7398 (m) REVERT: B 326 TYR cc_start: 0.7144 (m-80) cc_final: 0.6668 (m-80) REVERT: B 335 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.5497 (mtp85) REVERT: B 661 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7335 (ttt180) REVERT: B 799 MET cc_start: 0.8191 (mmp) cc_final: 0.7443 (mmm) outliers start: 47 outliers final: 31 residues processed: 229 average time/residue: 0.5636 time to fit residues: 144.5651 Evaluate side-chains 219 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.162317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123493 restraints weight = 20625.665| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.05 r_work: 0.3157 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17232 Z= 0.178 Angle : 0.543 7.602 23388 Z= 0.287 Chirality : 0.044 0.383 2568 Planarity : 0.004 0.043 3027 Dihedral : 6.332 78.774 2546 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.46 % Allowed : 23.85 % Favored : 72.69 % 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: 1.49 (0.19), residues: 2067 helix: 2.78 (0.19), residues: 696 sheet: 0.77 (0.24), residues: 516 loop : -0.39 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.012 0.001 TYR C 640 PHE 0.042 0.001 PHE C 508 TRP 0.004 0.001 TRP C 356 HIS 0.006 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00424 (17211) covalent geometry : angle 0.53372 (23340) SS BOND : bond 0.00547 ( 15) SS BOND : angle 1.56865 ( 30) hydrogen bonds : bond 0.05142 ( 835) hydrogen bonds : angle 5.08278 ( 2547) link_NAG-ASN : bond 0.00505 ( 6) link_NAG-ASN : angle 3.14016 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 232 MET cc_start: 0.7616 (mtp) cc_final: 0.6999 (mtp) REVERT: A 326 TYR cc_start: 0.7206 (m-80) cc_final: 0.6633 (m-80) REVERT: C 107 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.4715 (pm20) REVERT: C 138 GLU cc_start: 0.7113 (tp30) cc_final: 0.6249 (tp30) REVERT: C 321 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: C 326 TYR cc_start: 0.7163 (m-80) cc_final: 0.6878 (m-80) REVERT: B 138 GLU cc_start: 0.7046 (tp30) cc_final: 0.5808 (tp30) REVERT: B 325 PHE cc_start: 0.7083 (t80) cc_final: 0.6755 (t80) REVERT: B 326 TYR cc_start: 0.7203 (m-80) cc_final: 0.6739 (m-80) REVERT: B 664 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8505 (mm) outliers start: 61 outliers final: 29 residues processed: 239 average time/residue: 0.5664 time to fit residues: 151.6852 Evaluate side-chains 220 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN C 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123280 restraints weight = 20825.969| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.93 r_work: 0.3152 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17232 Z= 0.173 Angle : 0.536 7.374 23388 Z= 0.283 Chirality : 0.044 0.367 2568 Planarity : 0.004 0.040 3027 Dihedral : 5.593 63.277 2497 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.37 % Allowed : 22.88 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.18), residues: 2067 helix: 2.77 (0.19), residues: 696 sheet: 0.55 (0.22), residues: 543 loop : -0.47 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 132 TYR 0.012 0.001 TYR C 640 PHE 0.020 0.001 PHE C 508 TRP 0.005 0.001 TRP A 356 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00414 (17211) covalent geometry : angle 0.52570 (23340) SS BOND : bond 0.00603 ( 15) SS BOND : angle 1.78301 ( 30) hydrogen bonds : bond 0.05013 ( 835) hydrogen bonds : angle 4.81227 ( 2547) link_NAG-ASN : bond 0.00513 ( 6) link_NAG-ASN : angle 3.09245 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 198 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: A 232 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6856 (mtp) REVERT: A 326 TYR cc_start: 0.7191 (m-80) cc_final: 0.6577 (m-80) REVERT: A 607 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: A 664 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8396 (mm) REVERT: C 138 GLU cc_start: 0.7090 (tp30) cc_final: 0.6294 (tp30) REVERT: C 232 MET cc_start: 0.7863 (mtp) cc_final: 0.7638 (mtm) REVERT: C 321 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: C 326 TYR cc_start: 0.7198 (m-80) cc_final: 0.6740 (m-80) REVERT: C 385 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8232 (mtp180) REVERT: C 607 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: C 664 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8523 (mm) REVERT: C 799 MET cc_start: 0.8219 (mmp) cc_final: 0.7503 (mmm) REVERT: B 107 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.4948 (pm20) REVERT: B 138 GLU cc_start: 0.7109 (tp30) cc_final: 0.5827 (tp30) REVERT: B 325 PHE cc_start: 0.7091 (t80) cc_final: 0.6722 (t80) REVERT: B 326 TYR cc_start: 0.7209 (m-80) cc_final: 0.6871 (m-80) REVERT: B 607 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6628 (pt0) REVERT: B 799 MET cc_start: 0.8243 (mmp) cc_final: 0.7515 (mmm) outliers start: 77 outliers final: 37 residues processed: 254 average time/residue: 0.5519 time to fit residues: 157.2911 Evaluate side-chains 227 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123305 restraints weight = 20847.036| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.09 r_work: 0.3169 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17232 Z= 0.135 Angle : 0.500 7.122 23388 Z= 0.264 Chirality : 0.042 0.359 2568 Planarity : 0.003 0.031 3027 Dihedral : 5.377 54.880 2495 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.92 % Allowed : 23.17 % Favored : 72.91 % 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: 1.40 (0.18), residues: 2067 helix: 2.84 (0.19), residues: 699 sheet: 0.58 (0.22), residues: 543 loop : -0.50 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 132 TYR 0.011 0.001 TYR A 282 PHE 0.023 0.001 PHE A 508 TRP 0.004 0.001 TRP C 356 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00315 (17211) covalent geometry : angle 0.49165 (23340) SS BOND : bond 0.00485 ( 15) SS BOND : angle 1.26077 ( 30) hydrogen bonds : bond 0.04572 ( 835) hydrogen bonds : angle 4.58395 ( 2547) link_NAG-ASN : bond 0.00474 ( 6) link_NAG-ASN : angle 2.95566 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 193 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: A 178 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7480 (ptp90) REVERT: A 326 TYR cc_start: 0.7163 (m-80) cc_final: 0.6555 (m-80) REVERT: A 360 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5942 (mpp80) REVERT: A 508 PHE cc_start: 0.7448 (m-10) cc_final: 0.6780 (m-80) REVERT: A 607 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: A 664 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 799 MET cc_start: 0.8230 (mmp) cc_final: 0.7488 (mmm) REVERT: C 100 HIS cc_start: 0.7005 (m170) cc_final: 0.6648 (m170) REVERT: C 138 GLU cc_start: 0.7101 (tp30) cc_final: 0.6368 (tp30) REVERT: C 326 TYR cc_start: 0.7197 (m-80) cc_final: 0.6754 (m-80) REVERT: C 385 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8152 (mtp180) REVERT: C 508 PHE cc_start: 0.6208 (m-80) cc_final: 0.5946 (m-80) REVERT: C 607 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: C 664 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 107 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.4909 (pm20) REVERT: B 138 GLU cc_start: 0.7091 (tp30) cc_final: 0.5986 (tp30) REVERT: B 178 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7342 (ptp90) REVERT: B 325 PHE cc_start: 0.7143 (t80) cc_final: 0.6787 (t80) REVERT: B 326 TYR cc_start: 0.7201 (m-80) cc_final: 0.6852 (m-80) REVERT: B 607 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: B 664 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8438 (mm) outliers start: 69 outliers final: 36 residues processed: 246 average time/residue: 0.5501 time to fit residues: 151.7547 Evaluate side-chains 235 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 154 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 199 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN C 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124613 restraints weight = 20680.122| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.96 r_work: 0.3175 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17232 Z= 0.127 Angle : 0.492 7.099 23388 Z= 0.259 Chirality : 0.042 0.340 2568 Planarity : 0.003 0.031 3027 Dihedral : 5.017 50.809 2492 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.49 % Allowed : 22.66 % Favored : 72.86 % 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: 1.44 (0.18), residues: 2067 helix: 2.87 (0.19), residues: 699 sheet: 0.63 (0.22), residues: 543 loop : -0.52 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 132 TYR 0.011 0.001 TYR A 282 PHE 0.017 0.001 PHE B 508 TRP 0.004 0.001 TRP B 356 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00296 (17211) covalent geometry : angle 0.48366 (23340) SS BOND : bond 0.00424 ( 15) SS BOND : angle 1.26591 ( 30) hydrogen bonds : bond 0.04391 ( 835) hydrogen bonds : angle 4.45350 ( 2547) link_NAG-ASN : bond 0.00498 ( 6) link_NAG-ASN : angle 2.88369 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 192 time to evaluate : 0.645 Fit side-chains REVERT: A 172 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: A 178 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7493 (ptp90) REVERT: A 232 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6607 (mtp) REVERT: A 360 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5973 (mpp80) REVERT: A 508 PHE cc_start: 0.7426 (m-10) cc_final: 0.6762 (m-80) REVERT: A 607 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: A 799 MET cc_start: 0.8267 (mmp) cc_final: 0.7537 (mmm) REVERT: C 100 HIS cc_start: 0.7053 (m170) cc_final: 0.6671 (m170) REVERT: C 138 GLU cc_start: 0.7065 (tp30) cc_final: 0.6340 (tp30) REVERT: C 326 TYR cc_start: 0.7201 (m-80) cc_final: 0.6696 (m-80) REVERT: C 385 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8105 (mtp180) REVERT: C 411 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6049 (t70) REVERT: C 607 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6828 (pt0) REVERT: C 664 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8537 (mm) REVERT: C 799 MET cc_start: 0.8241 (mmp) cc_final: 0.7508 (mmm) REVERT: C 846 MET cc_start: 0.7931 (ttp) cc_final: 0.7640 (ttp) REVERT: B 138 GLU cc_start: 0.7076 (tp30) cc_final: 0.6095 (tp30) REVERT: B 178 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7380 (ptp90) REVERT: B 208 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6578 (mtm110) REVERT: B 232 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6786 (mtp) REVERT: B 242 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5875 (mmt90) REVERT: B 325 PHE cc_start: 0.7141 (t80) cc_final: 0.6786 (t80) REVERT: B 326 TYR cc_start: 0.7220 (m-80) cc_final: 0.6887 (m-80) REVERT: B 664 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8447 (mm) REVERT: B 799 MET cc_start: 0.8232 (mmp) cc_final: 0.7505 (mmm) outliers start: 79 outliers final: 36 residues processed: 250 average time/residue: 0.5483 time to fit residues: 153.2349 Evaluate side-chains 230 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN C 534 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.161793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122996 restraints weight = 20682.974| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.99 r_work: 0.3147 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17232 Z= 0.184 Angle : 0.540 8.277 23388 Z= 0.284 Chirality : 0.044 0.343 2568 Planarity : 0.004 0.042 3027 Dihedral : 5.112 50.974 2489 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.09 % Allowed : 23.11 % Favored : 72.80 % 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: 1.31 (0.18), residues: 2067 helix: 2.76 (0.19), residues: 702 sheet: 0.54 (0.22), residues: 543 loop : -0.58 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 132 TYR 0.012 0.001 TYR C 640 PHE 0.023 0.001 PHE B 508 TRP 0.004 0.001 TRP B 356 HIS 0.006 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00443 (17211) covalent geometry : angle 0.52992 (23340) SS BOND : bond 0.00572 ( 15) SS BOND : angle 1.80021 ( 30) hydrogen bonds : bond 0.04947 ( 835) hydrogen bonds : angle 4.52436 ( 2547) link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 3.16371 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: A 178 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7496 (ptp90) REVERT: A 232 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6713 (mtp) REVERT: A 360 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.5931 (mpp80) REVERT: A 508 PHE cc_start: 0.7488 (m-10) cc_final: 0.6812 (m-80) REVERT: A 607 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6738 (pt0) REVERT: A 664 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8444 (mm) REVERT: C 100 HIS cc_start: 0.7082 (m170) cc_final: 0.6691 (m170) REVERT: C 138 GLU cc_start: 0.7100 (tp30) cc_final: 0.6333 (tp30) REVERT: C 326 TYR cc_start: 0.7256 (m-80) cc_final: 0.6650 (m-80) REVERT: C 385 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8172 (mtp180) REVERT: C 607 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6851 (pt0) REVERT: C 664 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8534 (mm) REVERT: B 107 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.4728 (pm20) REVERT: B 138 GLU cc_start: 0.7152 (tp30) cc_final: 0.5958 (tp30) REVERT: B 178 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7435 (ptp90) REVERT: B 208 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6603 (mtm110) REVERT: B 242 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.5977 (mmt90) REVERT: B 325 PHE cc_start: 0.7216 (t80) cc_final: 0.6884 (t80) REVERT: B 326 TYR cc_start: 0.7250 (m-80) cc_final: 0.6904 (m-80) REVERT: B 607 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6776 (pt0) REVERT: B 799 MET cc_start: 0.8236 (mmp) cc_final: 0.7542 (mmm) outliers start: 72 outliers final: 40 residues processed: 234 average time/residue: 0.5616 time to fit residues: 146.9380 Evaluate side-chains 230 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 208 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 31 optimal weight: 0.0070 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN C 804 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126383 restraints weight = 20540.418| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.80 r_work: 0.3208 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17232 Z= 0.105 Angle : 0.472 6.728 23388 Z= 0.247 Chirality : 0.041 0.325 2568 Planarity : 0.003 0.033 3027 Dihedral : 4.770 49.421 2489 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.07 % Allowed : 23.79 % Favored : 73.14 % 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: 1.48 (0.18), residues: 2067 helix: 2.88 (0.19), residues: 702 sheet: 0.67 (0.22), residues: 543 loop : -0.50 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 132 TYR 0.012 0.001 TYR A 282 PHE 0.020 0.001 PHE B 508 TRP 0.004 0.001 TRP B 528 HIS 0.002 0.000 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00235 (17211) covalent geometry : angle 0.46422 (23340) SS BOND : bond 0.00352 ( 15) SS BOND : angle 1.22063 ( 30) hydrogen bonds : bond 0.04026 ( 835) hydrogen bonds : angle 4.33741 ( 2547) link_NAG-ASN : bond 0.00514 ( 6) link_NAG-ASN : angle 2.76150 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: A 178 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7469 (ptp90) REVERT: A 232 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6617 (mtp) REVERT: A 508 PHE cc_start: 0.7398 (m-10) cc_final: 0.6772 (m-80) REVERT: A 799 MET cc_start: 0.8194 (mmp) cc_final: 0.7458 (mmm) REVERT: C 138 GLU cc_start: 0.7067 (tp30) cc_final: 0.6324 (tp30) REVERT: C 326 TYR cc_start: 0.7220 (m-80) cc_final: 0.6697 (m-80) REVERT: C 385 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8028 (mtp180) REVERT: C 664 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8484 (mm) REVERT: C 799 MET cc_start: 0.8206 (mmp) cc_final: 0.7467 (mmm) REVERT: B 107 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.4798 (pm20) REVERT: B 138 GLU cc_start: 0.7112 (tp30) cc_final: 0.5919 (tp30) REVERT: B 208 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6502 (mtm110) REVERT: B 325 PHE cc_start: 0.7123 (t80) cc_final: 0.6819 (t80) REVERT: B 326 TYR cc_start: 0.7227 (m-80) cc_final: 0.6919 (m-80) REVERT: B 385 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8254 (mtp180) REVERT: B 407 VAL cc_start: 0.8491 (m) cc_final: 0.8238 (t) REVERT: B 664 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8412 (mm) REVERT: B 799 MET cc_start: 0.8230 (mmp) cc_final: 0.7542 (mmm) outliers start: 54 outliers final: 27 residues processed: 229 average time/residue: 0.5676 time to fit residues: 145.2339 Evaluate side-chains 210 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125513 restraints weight = 20694.415| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.95 r_work: 0.3161 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17232 Z= 0.144 Angle : 0.505 7.356 23388 Z= 0.265 Chirality : 0.043 0.324 2568 Planarity : 0.003 0.033 3027 Dihedral : 4.853 49.661 2488 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.18 % Allowed : 23.68 % Favored : 73.14 % 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: 1.44 (0.18), residues: 2067 helix: 2.86 (0.19), residues: 702 sheet: 0.65 (0.22), residues: 543 loop : -0.52 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 132 TYR 0.018 0.001 TYR C 265 PHE 0.022 0.001 PHE B 508 TRP 0.005 0.001 TRP C 539 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00340 (17211) covalent geometry : angle 0.49585 (23340) SS BOND : bond 0.00501 ( 15) SS BOND : angle 1.48386 ( 30) hydrogen bonds : bond 0.04467 ( 835) hydrogen bonds : angle 4.37132 ( 2547) link_NAG-ASN : bond 0.00486 ( 6) link_NAG-ASN : angle 2.88874 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: A 178 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7421 (ptp90) REVERT: A 232 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6694 (mtp) REVERT: A 664 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 799 MET cc_start: 0.8182 (mmp) cc_final: 0.7408 (mmm) REVERT: C 100 HIS cc_start: 0.6840 (m170) cc_final: 0.6573 (m170) REVERT: C 138 GLU cc_start: 0.6943 (tp30) cc_final: 0.6354 (tp30) REVERT: C 326 TYR cc_start: 0.7168 (m-80) cc_final: 0.6607 (m-80) REVERT: C 385 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7941 (mtp180) REVERT: C 607 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: C 664 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8478 (mm) REVERT: C 799 MET cc_start: 0.8179 (mmp) cc_final: 0.7406 (mmm) REVERT: B 107 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.4895 (pm20) REVERT: B 138 GLU cc_start: 0.7042 (tp30) cc_final: 0.5897 (tp30) REVERT: B 178 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7453 (ptp90) REVERT: B 208 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6440 (mtm110) REVERT: B 242 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5816 (mmt90) REVERT: B 326 TYR cc_start: 0.7166 (m-80) cc_final: 0.6907 (m-80) REVERT: B 385 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8144 (mtp180) REVERT: B 407 VAL cc_start: 0.8546 (m) cc_final: 0.8307 (t) REVERT: B 607 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6710 (pt0) outliers start: 56 outliers final: 32 residues processed: 224 average time/residue: 0.6098 time to fit residues: 151.8507 Evaluate side-chains 219 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 45 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.163368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124688 restraints weight = 20606.026| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.09 r_work: 0.3169 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17232 Z= 0.136 Angle : 0.502 7.672 23388 Z= 0.262 Chirality : 0.042 0.329 2568 Planarity : 0.003 0.033 3027 Dihedral : 4.831 48.728 2488 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.07 % Allowed : 23.62 % Favored : 73.31 % 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: 1.43 (0.18), residues: 2067 helix: 2.84 (0.19), residues: 702 sheet: 0.64 (0.22), residues: 543 loop : -0.52 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 132 TYR 0.013 0.001 TYR A 265 PHE 0.030 0.001 PHE A 508 TRP 0.004 0.001 TRP C 356 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00321 (17211) covalent geometry : angle 0.49330 (23340) SS BOND : bond 0.00451 ( 15) SS BOND : angle 1.33940 ( 30) hydrogen bonds : bond 0.04406 ( 835) hydrogen bonds : angle 4.34927 ( 2547) link_NAG-ASN : bond 0.00486 ( 6) link_NAG-ASN : angle 2.91620 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: A 178 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7411 (ptp90) REVERT: A 232 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6678 (mtp) REVERT: A 508 PHE cc_start: 0.7448 (m-10) cc_final: 0.6838 (m-80) REVERT: A 607 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6579 (pt0) REVERT: A 664 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8367 (mm) REVERT: A 799 MET cc_start: 0.8174 (mmp) cc_final: 0.7412 (mmm) REVERT: C 100 HIS cc_start: 0.6888 (m170) cc_final: 0.6588 (m170) REVERT: C 138 GLU cc_start: 0.6899 (tp30) cc_final: 0.6259 (tp30) REVERT: C 326 TYR cc_start: 0.7130 (m-80) cc_final: 0.6580 (m-80) REVERT: C 385 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7921 (mtp180) REVERT: C 664 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8452 (mm) REVERT: C 799 MET cc_start: 0.8194 (mmp) cc_final: 0.7436 (mmm) REVERT: B 107 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.4916 (pm20) REVERT: B 138 GLU cc_start: 0.7014 (tp30) cc_final: 0.5863 (tp30) REVERT: B 178 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7482 (ptp90) REVERT: B 208 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6440 (mtm110) REVERT: B 242 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5760 (mmt90) REVERT: B 326 TYR cc_start: 0.7162 (m-80) cc_final: 0.6885 (m-80) REVERT: B 385 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8134 (mtp180) REVERT: B 607 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6703 (pt0) REVERT: B 799 MET cc_start: 0.8110 (mmp) cc_final: 0.7405 (mmm) outliers start: 54 outliers final: 38 residues processed: 222 average time/residue: 0.5787 time to fit residues: 142.9313 Evaluate side-chains 224 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 11 optimal weight: 0.0030 chunk 60 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 163 optimal weight: 0.0040 chunk 173 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.164834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126134 restraints weight = 20459.000| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.79 r_work: 0.3206 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17232 Z= 0.107 Angle : 0.479 7.118 23388 Z= 0.250 Chirality : 0.041 0.319 2568 Planarity : 0.003 0.029 3027 Dihedral : 4.680 48.122 2488 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.90 % Allowed : 23.91 % Favored : 73.20 % 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: 1.51 (0.18), residues: 2067 helix: 2.95 (0.19), residues: 699 sheet: 0.68 (0.22), residues: 543 loop : -0.50 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 132 TYR 0.013 0.001 TYR B 282 PHE 0.025 0.001 PHE A 508 TRP 0.004 0.001 TRP A 354 HIS 0.002 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00242 (17211) covalent geometry : angle 0.47205 (23340) SS BOND : bond 0.00382 ( 15) SS BOND : angle 1.10624 ( 30) hydrogen bonds : bond 0.04045 ( 835) hydrogen bonds : angle 4.26854 ( 2547) link_NAG-ASN : bond 0.00497 ( 6) link_NAG-ASN : angle 2.72563 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4134 Ramachandran restraints generated. 2067 Oldfield, 0 Emsley, 2067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: A 178 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7417 (ptp90) REVERT: A 232 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6675 (mtp) REVERT: A 664 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 799 MET cc_start: 0.8216 (mmp) cc_final: 0.7467 (mmm) REVERT: C 100 HIS cc_start: 0.6858 (m170) cc_final: 0.6556 (m170) REVERT: C 138 GLU cc_start: 0.6992 (tp30) cc_final: 0.6237 (tp30) REVERT: C 326 TYR cc_start: 0.7214 (m-80) cc_final: 0.6576 (m-80) REVERT: C 385 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8014 (mtp180) REVERT: C 664 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8484 (mm) REVERT: C 799 MET cc_start: 0.8246 (mmp) cc_final: 0.7476 (mmm) REVERT: C 846 MET cc_start: 0.7750 (ttp) cc_final: 0.7399 (ttp) REVERT: B 107 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.4739 (pm20) REVERT: B 138 GLU cc_start: 0.7053 (tp30) cc_final: 0.5862 (tp30) REVERT: B 178 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7502 (ptp90) REVERT: B 232 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6748 (mtp) REVERT: B 321 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: B 326 TYR cc_start: 0.7271 (m-80) cc_final: 0.6980 (m-80) REVERT: B 385 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8254 (mtp180) REVERT: B 664 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8440 (mm) REVERT: B 799 MET cc_start: 0.8173 (mmp) cc_final: 0.7416 (mmm) outliers start: 51 outliers final: 34 residues processed: 213 average time/residue: 0.6055 time to fit residues: 143.4024 Evaluate side-chains 215 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 845 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 186 optimal weight: 0.9990 chunk 196 optimal weight: 0.0670 chunk 179 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.163885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125522 restraints weight = 20605.099| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.02 r_work: 0.3194 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17232 Z= 0.132 Angle : 0.500 7.180 23388 Z= 0.261 Chirality : 0.042 0.319 2568 Planarity : 0.003 0.029 3027 Dihedral : 4.746 48.388 2488 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.07 % Allowed : 23.79 % Favored : 73.14 % 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: 1.47 (0.18), residues: 2067 helix: 2.90 (0.19), residues: 699 sheet: 0.66 (0.22), residues: 543 loop : -0.51 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 132 TYR 0.012 0.001 TYR A 265 PHE 0.028 0.001 PHE A 508 TRP 0.004 0.001 TRP C 356 HIS 0.003 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00309 (17211) covalent geometry : angle 0.49221 (23340) SS BOND : bond 0.00455 ( 15) SS BOND : angle 1.30484 ( 30) hydrogen bonds : bond 0.04317 ( 835) hydrogen bonds : angle 4.29733 ( 2547) link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 2.80130 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6436.25 seconds wall clock time: 109 minutes 56.92 seconds (6596.92 seconds total)