Starting phenix.real_space_refine on Mon Apr 6 01:12:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5v_47529/04_2026/9e5v_47529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5v_47529/04_2026/9e5v_47529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e5v_47529/04_2026/9e5v_47529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5v_47529/04_2026/9e5v_47529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e5v_47529/04_2026/9e5v_47529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5v_47529/04_2026/9e5v_47529.map" } resolution = 2.45 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= 0.040 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 66 5.16 5 C 9027 2.51 5 N 2517 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 14319 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 562} Chain breaks: 1 Chain: "B" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 562} Chain breaks: 1 Chain: "C" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.12, per 1000 atoms: 0.22 Number of scatterers: 14319 At special positions: 0 Unit cell: (98.34, 95.04, 180.84, 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 66 16.00 O 2709 8.00 N 2517 7.00 C 9027 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=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 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=2.03 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=2.04 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=2.03 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 674 " " NAG B1001 " - " ASN B 674 " " NAG C1001 " - " ASN C 674 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 515.6 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3354 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 36 sheets defined 22.4% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... 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 306 through 310 removed outlier: 4.020A pdb=" N THR A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) No H-bonds generated for '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 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 4.157A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 535 Processing helix chain 'A' and resid 535 through 546 removed outlier: 4.137A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 545 " --> pdb=" O GLU A 541 " (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 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 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 306 through 310 removed outlier: 3.981A pdb=" N THR B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) No H-bonds generated for '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 407 Processing helix chain 'B' and resid 411 through 429 removed outlier: 4.135A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 535 Processing helix chain 'B' and resid 535 through 546 removed outlier: 4.123A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (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 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 717 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 306 through 310 removed outlier: 3.933A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 310 " --> pdb=" O SER C 307 " (cutoff:3.500A) No H-bonds generated for '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 407 Processing helix chain 'C' and resid 411 through 429 removed outlier: 4.157A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 535 Processing helix chain 'C' and resid 535 through 546 removed outlier: 4.139A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (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 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 711 through 717 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: 6.646A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.583A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.583A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 191 removed outlier: 6.487A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.241A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG A 342 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP A 323 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 344 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLN A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 346 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.090A 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 375 through 380 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 removed outlier: 4.039A pdb=" N CYS A 596 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 631 " --> pdb=" O CYS A 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.759A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.108A 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: 3.562A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.566A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.566A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 180 through 191 removed outlier: 6.469A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.235A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG B 342 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP B 323 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU B 344 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLN B 321 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR B 346 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE B 319 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC2, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC3, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC4, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC5, first strand: chain 'B' and resid 595 through 597 removed outlier: 4.097A pdb=" N CYS B 596 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 631 " --> pdb=" O CYS B 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 643 removed outlier: 6.459A pdb=" N TYR B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN B 658 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 649 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.522A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 567 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC9, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.565A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.565A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 180 through 191 removed outlier: 6.510A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU C 187 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL C 168 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG C 189 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS C 166 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N TYR C 164 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.216A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG C 342 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP C 323 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU C 344 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN C 321 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR C 346 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE C 319 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD5, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD6, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AD7, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AD8, first strand: chain 'C' and resid 595 through 597 removed outlier: 4.073A pdb=" N CYS C 596 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 631 " --> pdb=" O CYS C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 638 through 643 removed outlier: 6.518A pdb=" N TYR C 647 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN C 658 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR C 649 " --> pdb=" O SER C 656 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.56 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: 4775 1.34 - 1.46: 3639 1.46 - 1.58: 6157 1.58 - 1.71: 0 1.71 - 1.83: 102 Bond restraints: 14673 Sorted by residual: bond pdb=" N HIS A 724 " pdb=" CA HIS A 724 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.20e-02 6.94e+03 3.38e+00 bond pdb=" N HIS B 724 " pdb=" CA HIS B 724 " ideal model delta sigma weight residual 1.462 1.482 -0.021 1.28e-02 6.10e+03 2.60e+00 bond pdb=" N GLY C 565 " pdb=" CA GLY C 565 " ideal model delta sigma weight residual 1.460 1.446 0.015 1.26e-02 6.30e+03 1.36e+00 bond pdb=" C ALA B 725 " pdb=" O ALA B 725 " ideal model delta sigma weight residual 1.231 1.254 -0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" CG HIS A 724 " pdb=" CD2 HIS A 724 " ideal model delta sigma weight residual 1.354 1.342 0.012 1.10e-02 8.26e+03 1.22e+00 ... (remaining 14668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 19659 1.42 - 2.85: 240 2.85 - 4.27: 37 4.27 - 5.69: 1 5.69 - 7.12: 1 Bond angle restraints: 19938 Sorted by residual: angle pdb=" CA HIS B 724 " pdb=" CB HIS B 724 " pdb=" CG HIS B 724 " ideal model delta sigma weight residual 113.80 110.73 3.07 1.00e+00 1.00e+00 9.43e+00 angle pdb=" CA HIS A 724 " pdb=" CB HIS A 724 " pdb=" CG HIS A 724 " ideal model delta sigma weight residual 113.80 110.79 3.01 1.00e+00 1.00e+00 9.08e+00 angle pdb=" CB GLN A 584 " pdb=" CG GLN A 584 " pdb=" CD GLN A 584 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.70e+00 3.46e-01 6.56e+00 angle pdb=" N ILE B 719 " pdb=" CA ILE B 719 " pdb=" CB ILE B 719 " ideal model delta sigma weight residual 112.21 109.49 2.72 1.10e+00 8.26e-01 6.10e+00 angle pdb=" N ILE A 719 " pdb=" CA ILE A 719 " pdb=" CB ILE A 719 " ideal model delta sigma weight residual 112.21 109.51 2.70 1.10e+00 8.26e-01 6.03e+00 ... (remaining 19933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7584 17.54 - 35.08: 904 35.08 - 52.62: 248 52.62 - 70.16: 45 70.16 - 87.70: 24 Dihedral angle restraints: 8805 sinusoidal: 3591 harmonic: 5214 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 633 " pdb=" CB CYS A 633 " ideal model delta sinusoidal sigma weight residual 93.00 39.05 53.95 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS B 271 " pdb=" CB CYS B 271 " ideal model delta sinusoidal sigma weight residual 93.00 59.68 33.32 1 1.00e+01 1.00e-02 1.58e+01 dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS C 271 " pdb=" CB CYS C 271 " ideal model delta sinusoidal sigma weight residual 93.00 59.82 33.18 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 8802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1345 0.030 - 0.060: 551 0.060 - 0.090: 136 0.090 - 0.120: 122 0.120 - 0.150: 18 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CA MET A 421 " pdb=" N MET A 421 " pdb=" C MET A 421 " pdb=" CB MET A 421 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE B 146 " pdb=" N ILE B 146 " pdb=" C ILE B 146 " pdb=" CB ILE B 146 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 146 " pdb=" N ILE A 146 " pdb=" C ILE A 146 " pdb=" CB ILE A 146 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 2169 not shown) Planarity restraints: 2607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 723 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C ILE A 723 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 723 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS A 724 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 723 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C ILE B 723 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 723 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS B 724 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 347 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO C 348 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " 0.026 5.00e-02 4.00e+02 ... (remaining 2604 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3311 2.80 - 3.32: 11382 3.32 - 3.85: 23632 3.85 - 4.37: 28492 4.37 - 4.90: 49766 Nonbonded interactions: 116583 Sorted by model distance: nonbonded pdb=" OD1 ASP A 680 " pdb=" NE2 GLN B 514 " model vdw 2.271 3.120 nonbonded pdb=" NE2 GLN A 514 " pdb=" OD1 ASP C 680 " model vdw 2.273 3.120 nonbonded pdb=" OH TYR C 282 " pdb=" OD2 ASP C 408 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP B 680 " pdb=" NE2 GLN C 514 " model vdw 2.279 3.120 nonbonded pdb=" OH TYR A 282 " pdb=" OD2 ASP A 408 " model vdw 2.282 3.040 ... (remaining 116578 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: 24.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 0.031 14691 Z= 0.118 Angle : 0.451 7.117 19977 Z= 0.258 Chirality : 0.041 0.150 2172 Planarity : 0.004 0.047 2604 Dihedral : 16.711 87.699 5406 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.95 % Allowed : 19.86 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.19), residues: 1758 helix: 1.71 (0.30), residues: 309 sheet: 0.91 (0.22), residues: 507 loop : -0.24 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 627 TYR 0.019 0.001 TYR C 655 PHE 0.014 0.001 PHE B 287 TRP 0.008 0.001 TRP B 354 HIS 0.003 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00252 (14673) covalent geometry : angle 0.44799 (19938) SS BOND : bond 0.00405 ( 15) SS BOND : angle 0.97494 ( 30) hydrogen bonds : bond 0.15234 ( 542) hydrogen bonds : angle 7.08432 ( 1713) link_NAG-ASN : bond 0.00232 ( 3) link_NAG-ASN : angle 1.68317 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8081 (pp20) cc_final: 0.7356 (mp0) REVERT: A 233 GLU cc_start: 0.8205 (tp30) cc_final: 0.7936 (tp30) REVERT: A 320 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8270 (ttpt) REVERT: A 415 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7529 (mmtp) REVERT: A 515 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7934 (mtm110) REVERT: A 628 ASP cc_start: 0.7311 (p0) cc_final: 0.6997 (p0) REVERT: A 652 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 679 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: B 112 ASN cc_start: 0.8113 (p0) cc_final: 0.7854 (p0) REVERT: B 136 ARG cc_start: 0.7067 (mtp180) cc_final: 0.6820 (mtt180) REVERT: B 167 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: B 187 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 195 GLU cc_start: 0.8001 (pp20) cc_final: 0.7277 (mp0) REVERT: B 233 GLU cc_start: 0.8258 (tp30) cc_final: 0.8016 (tp30) REVERT: B 320 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8371 (tttt) REVERT: B 415 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7403 (mmtp) REVERT: B 496 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8201 (mmtm) REVERT: B 614 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7635 (mm-30) REVERT: B 628 ASP cc_start: 0.7419 (p0) cc_final: 0.7071 (p0) REVERT: B 652 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 679 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 195 GLU cc_start: 0.8025 (pp20) cc_final: 0.7236 (mp0) REVERT: C 219 GLU cc_start: 0.8799 (tt0) cc_final: 0.8460 (mm-30) REVERT: C 233 GLU cc_start: 0.8154 (tp30) cc_final: 0.7937 (tp30) REVERT: C 320 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8354 (tttt) REVERT: C 335 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8299 (ttp80) REVERT: C 380 TYR cc_start: 0.7076 (t80) cc_final: 0.6608 (t80) REVERT: C 415 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7462 (mptt) REVERT: C 562 ARG cc_start: 0.8482 (mtp180) cc_final: 0.8160 (mtm110) REVERT: C 628 ASP cc_start: 0.7621 (p0) cc_final: 0.7203 (p0) REVERT: C 652 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 679 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: C 695 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7774 (ttmt) outliers start: 30 outliers final: 21 residues processed: 209 average time/residue: 0.8540 time to fit residues: 190.6934 Evaluate side-chains 213 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 308 HIS B 580 ASN C 308 HIS C 580 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.090774 restraints weight = 15254.466| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.77 r_work: 0.2876 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14691 Z= 0.246 Angle : 0.581 10.248 19977 Z= 0.321 Chirality : 0.048 0.157 2172 Planarity : 0.005 0.054 2604 Dihedral : 6.846 60.790 2110 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 4.04 % Allowed : 16.80 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1758 helix: 1.35 (0.30), residues: 318 sheet: 0.78 (0.22), residues: 510 loop : -0.31 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 208 TYR 0.014 0.002 TYR A 653 PHE 0.026 0.002 PHE B 287 TRP 0.009 0.002 TRP B 354 HIS 0.006 0.002 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00588 (14673) covalent geometry : angle 0.57782 (19938) SS BOND : bond 0.00789 ( 15) SS BOND : angle 1.27543 ( 30) hydrogen bonds : bond 0.05892 ( 542) hydrogen bonds : angle 5.54277 ( 1713) link_NAG-ASN : bond 0.00383 ( 3) link_NAG-ASN : angle 1.90579 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.501 Fit side-chains REVERT: A 195 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 233 GLU cc_start: 0.8185 (tp30) cc_final: 0.7960 (tp30) REVERT: A 320 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8370 (ttpt) REVERT: A 415 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7573 (mptt) REVERT: A 628 ASP cc_start: 0.7394 (p0) cc_final: 0.7086 (p0) REVERT: A 652 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 679 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: B 136 ARG cc_start: 0.7120 (mtp180) cc_final: 0.6912 (mmt180) REVERT: B 187 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: B 195 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: B 233 GLU cc_start: 0.8289 (tp30) cc_final: 0.8061 (tp30) REVERT: B 244 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8874 (m) REVERT: B 320 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8475 (tttt) REVERT: B 415 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7398 (mmtp) REVERT: B 496 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8240 (mmtm) REVERT: B 628 ASP cc_start: 0.7495 (p0) cc_final: 0.7115 (p0) REVERT: B 652 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 679 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: C 195 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: C 219 GLU cc_start: 0.8826 (tt0) cc_final: 0.8500 (mm-30) REVERT: C 233 GLU cc_start: 0.8165 (tp30) cc_final: 0.7942 (tp30) REVERT: C 320 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8419 (tttt) REVERT: C 328 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7887 (ttp80) REVERT: C 415 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7549 (mptt) REVERT: C 652 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7599 (mm-30) REVERT: C 661 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7583 (mtt-85) REVERT: C 679 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: C 695 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7704 (tttt) outliers start: 62 outliers final: 30 residues processed: 234 average time/residue: 0.7925 time to fit residues: 199.1531 Evaluate side-chains 226 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 308 HIS B 580 ASN C 580 ASN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.090179 restraints weight = 15321.163| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.76 r_work: 0.2865 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 14691 Z= 0.275 Angle : 0.609 10.160 19977 Z= 0.336 Chirality : 0.049 0.173 2172 Planarity : 0.006 0.057 2604 Dihedral : 6.559 64.123 2090 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.21 % Allowed : 16.15 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1758 helix: 1.47 (0.30), residues: 300 sheet: 0.58 (0.21), residues: 540 loop : -0.53 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.022 0.002 TYR B 655 PHE 0.029 0.002 PHE B 287 TRP 0.011 0.003 TRP C 356 HIS 0.006 0.002 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00661 (14673) covalent geometry : angle 0.60421 (19938) SS BOND : bond 0.00951 ( 15) SS BOND : angle 1.72578 ( 30) hydrogen bonds : bond 0.05981 ( 542) hydrogen bonds : angle 5.46064 ( 1713) link_NAG-ASN : bond 0.00384 ( 3) link_NAG-ASN : angle 2.10534 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 187 time to evaluate : 0.596 Fit side-chains REVERT: A 195 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: A 233 GLU cc_start: 0.8185 (tp30) cc_final: 0.7954 (tp30) REVERT: A 320 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8353 (ttpt) REVERT: A 415 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7604 (mptt) REVERT: A 628 ASP cc_start: 0.7552 (p0) cc_final: 0.7237 (p0) REVERT: A 652 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 679 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: B 187 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: B 195 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: B 233 GLU cc_start: 0.8306 (tp30) cc_final: 0.8053 (tp30) REVERT: B 320 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8454 (tttt) REVERT: B 415 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7507 (mptt) REVERT: B 496 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8245 (mmtm) REVERT: B 628 ASP cc_start: 0.7563 (p0) cc_final: 0.7154 (p0) REVERT: B 652 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 661 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7571 (mtp-110) REVERT: C 195 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: C 219 GLU cc_start: 0.8812 (tt0) cc_final: 0.8470 (mm-30) REVERT: C 233 GLU cc_start: 0.8164 (tp30) cc_final: 0.7930 (tp30) REVERT: C 320 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8425 (tttt) REVERT: C 328 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7882 (ttp80) REVERT: C 332 THR cc_start: 0.8705 (m) cc_final: 0.8452 (p) REVERT: C 335 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8250 (ttp-170) REVERT: C 377 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7337 (ttt180) REVERT: C 415 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7563 (mptt) REVERT: C 652 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7527 (mm-30) REVERT: C 661 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7674 (mtp-110) REVERT: C 679 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: C 695 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7727 (ttmt) outliers start: 80 outliers final: 47 residues processed: 240 average time/residue: 0.8014 time to fit residues: 206.2370 Evaluate side-chains 243 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 107 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.092546 restraints weight = 15293.840| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.77 r_work: 0.2906 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14691 Z= 0.128 Angle : 0.476 9.057 19977 Z= 0.265 Chirality : 0.042 0.130 2172 Planarity : 0.004 0.054 2604 Dihedral : 6.059 58.362 2090 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 3.45 % Allowed : 18.36 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1758 helix: 1.39 (0.29), residues: 318 sheet: 0.74 (0.21), residues: 510 loop : -0.36 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 627 TYR 0.019 0.001 TYR A 655 PHE 0.020 0.001 PHE A 287 TRP 0.010 0.002 TRP B 354 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00292 (14673) covalent geometry : angle 0.47321 (19938) SS BOND : bond 0.00519 ( 15) SS BOND : angle 1.06158 ( 30) hydrogen bonds : bond 0.04744 ( 542) hydrogen bonds : angle 5.11410 ( 1713) link_NAG-ASN : bond 0.00264 ( 3) link_NAG-ASN : angle 1.70281 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.549 Fit side-chains REVERT: A 138 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6213 (tt0) REVERT: A 195 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 233 GLU cc_start: 0.8132 (tp30) cc_final: 0.7919 (tp30) REVERT: A 320 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8373 (ttpt) REVERT: A 415 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7540 (mmtp) REVERT: A 628 ASP cc_start: 0.7547 (p0) cc_final: 0.7218 (p0) REVERT: A 652 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 679 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: B 187 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: B 195 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 233 GLU cc_start: 0.8266 (tp30) cc_final: 0.8042 (tp30) REVERT: B 320 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8474 (tttt) REVERT: B 415 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7348 (mmtp) REVERT: B 496 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8262 (mmtm) REVERT: B 628 ASP cc_start: 0.7576 (p0) cc_final: 0.7171 (p0) REVERT: B 652 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7591 (mm-30) REVERT: C 195 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: C 219 GLU cc_start: 0.8764 (tt0) cc_final: 0.8487 (mm-30) REVERT: C 233 GLU cc_start: 0.8149 (tp30) cc_final: 0.7937 (tp30) REVERT: C 320 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8424 (tttt) REVERT: C 332 THR cc_start: 0.8660 (m) cc_final: 0.8439 (p) REVERT: C 415 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7483 (mptt) REVERT: C 652 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7586 (mm-30) REVERT: C 679 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: C 695 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7737 (ttmt) outliers start: 53 outliers final: 34 residues processed: 224 average time/residue: 0.7602 time to fit residues: 183.5612 Evaluate side-chains 225 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 169 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN C 657 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091930 restraints weight = 15519.943| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.58 r_work: 0.2893 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 14691 Z= 0.270 Angle : 0.598 10.121 19977 Z= 0.329 Chirality : 0.049 0.171 2172 Planarity : 0.005 0.057 2604 Dihedral : 6.455 63.659 2089 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.69 % Allowed : 17.12 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1758 helix: 1.51 (0.30), residues: 300 sheet: 0.57 (0.21), residues: 540 loop : -0.55 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 208 TYR 0.015 0.002 TYR C 254 PHE 0.028 0.002 PHE B 287 TRP 0.010 0.003 TRP C 356 HIS 0.006 0.002 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00650 (14673) covalent geometry : angle 0.59312 (19938) SS BOND : bond 0.00933 ( 15) SS BOND : angle 1.71819 ( 30) hydrogen bonds : bond 0.05808 ( 542) hydrogen bonds : angle 5.33541 ( 1713) link_NAG-ASN : bond 0.00408 ( 3) link_NAG-ASN : angle 1.98745 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 179 time to evaluate : 0.583 Fit side-chains REVERT: A 138 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6220 (tt0) REVERT: A 195 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: A 233 GLU cc_start: 0.8045 (tp30) cc_final: 0.7768 (tp30) REVERT: A 320 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8293 (tttt) REVERT: A 415 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7352 (mmtp) REVERT: A 628 ASP cc_start: 0.7478 (p0) cc_final: 0.7141 (p0) REVERT: A 652 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 679 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: B 187 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: B 195 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: B 233 GLU cc_start: 0.8158 (tp30) cc_final: 0.7882 (tp30) REVERT: B 320 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8284 (tttt) REVERT: B 415 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7309 (mptt) REVERT: B 496 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8150 (mmtm) REVERT: B 628 ASP cc_start: 0.7546 (p0) cc_final: 0.7126 (p0) REVERT: B 652 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7435 (mm-30) REVERT: C 195 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: C 219 GLU cc_start: 0.8767 (tt0) cc_final: 0.8413 (mm-30) REVERT: C 233 GLU cc_start: 0.8056 (tp30) cc_final: 0.7794 (tp30) REVERT: C 320 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8258 (tttt) REVERT: C 332 THR cc_start: 0.8662 (m) cc_final: 0.8429 (p) REVERT: C 415 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7393 (mptt) REVERT: C 652 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7544 (mm-30) REVERT: C 679 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: C 695 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7567 (ttmt) outliers start: 72 outliers final: 49 residues processed: 232 average time/residue: 0.7926 time to fit residues: 197.5671 Evaluate side-chains 237 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 72 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 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 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093415 restraints weight = 15567.308| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.52 r_work: 0.2917 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14691 Z= 0.184 Angle : 0.527 9.547 19977 Z= 0.292 Chirality : 0.045 0.136 2172 Planarity : 0.005 0.056 2604 Dihedral : 6.281 61.486 2089 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 4.62 % Allowed : 17.12 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1758 helix: 1.61 (0.30), residues: 300 sheet: 0.59 (0.21), residues: 540 loop : -0.54 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 627 TYR 0.021 0.002 TYR A 655 PHE 0.024 0.002 PHE B 287 TRP 0.010 0.002 TRP B 354 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00436 (14673) covalent geometry : angle 0.52366 (19938) SS BOND : bond 0.00699 ( 15) SS BOND : angle 1.33796 ( 30) hydrogen bonds : bond 0.05208 ( 542) hydrogen bonds : angle 5.19804 ( 1713) link_NAG-ASN : bond 0.00331 ( 3) link_NAG-ASN : angle 1.84421 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 0.573 Fit side-chains REVERT: A 138 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6202 (tt0) REVERT: A 195 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 233 GLU cc_start: 0.8060 (tp30) cc_final: 0.7821 (tp30) REVERT: A 320 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8360 (tttt) REVERT: A 415 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7429 (mmtp) REVERT: A 628 ASP cc_start: 0.7553 (p0) cc_final: 0.7231 (p0) REVERT: A 652 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 679 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: B 187 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: B 195 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 233 GLU cc_start: 0.8144 (tp30) cc_final: 0.7904 (tp30) REVERT: B 320 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8351 (tttt) REVERT: B 415 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7285 (mmtp) REVERT: B 496 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8209 (mmtm) REVERT: B 627 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7136 (mtp85) REVERT: B 628 ASP cc_start: 0.7601 (p0) cc_final: 0.7190 (p0) REVERT: B 652 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 661 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7545 (mtt-85) REVERT: C 195 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: C 219 GLU cc_start: 0.8746 (tt0) cc_final: 0.8445 (mm-30) REVERT: C 233 GLU cc_start: 0.8043 (tp30) cc_final: 0.7819 (tp30) REVERT: C 320 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8317 (tttt) REVERT: C 377 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7287 (ttt180) REVERT: C 415 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7436 (mptt) REVERT: C 652 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 679 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: C 695 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7568 (tttt) outliers start: 71 outliers final: 46 residues processed: 233 average time/residue: 0.7704 time to fit residues: 192.9698 Evaluate side-chains 238 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 139 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093851 restraints weight = 15322.009| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.61 r_work: 0.2921 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14691 Z= 0.148 Angle : 0.489 9.015 19977 Z= 0.271 Chirality : 0.043 0.133 2172 Planarity : 0.005 0.055 2604 Dihedral : 6.065 58.142 2089 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 4.43 % Allowed : 17.25 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1758 helix: 1.36 (0.29), residues: 318 sheet: 0.73 (0.21), residues: 510 loop : -0.38 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 627 TYR 0.022 0.001 TYR A 655 PHE 0.021 0.002 PHE B 287 TRP 0.010 0.002 TRP B 354 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00344 (14673) covalent geometry : angle 0.48631 (19938) SS BOND : bond 0.00582 ( 15) SS BOND : angle 1.14045 ( 30) hydrogen bonds : bond 0.04828 ( 542) hydrogen bonds : angle 5.07710 ( 1713) link_NAG-ASN : bond 0.00279 ( 3) link_NAG-ASN : angle 1.73313 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 0.542 Fit side-chains REVERT: A 138 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6213 (tt0) REVERT: A 195 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 233 GLU cc_start: 0.8031 (tp30) cc_final: 0.7783 (tp30) REVERT: A 320 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8337 (tttt) REVERT: A 415 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7411 (mmtp) REVERT: A 628 ASP cc_start: 0.7509 (p0) cc_final: 0.7183 (p0) REVERT: A 652 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 679 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: B 187 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: B 195 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: B 233 GLU cc_start: 0.8142 (tp30) cc_final: 0.7890 (tp30) REVERT: B 320 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8339 (tttt) REVERT: B 415 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7236 (mmtp) REVERT: B 496 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8193 (mmtm) REVERT: B 627 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7165 (mtp85) REVERT: B 652 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 661 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7363 (mtp-110) REVERT: C 195 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: C 219 GLU cc_start: 0.8738 (tt0) cc_final: 0.8431 (mm-30) REVERT: C 233 GLU cc_start: 0.8051 (tp30) cc_final: 0.7817 (tp30) REVERT: C 320 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8306 (tttt) REVERT: C 415 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7380 (mptt) REVERT: C 652 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7512 (mm-30) REVERT: C 679 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: C 695 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7550 (tttt) outliers start: 68 outliers final: 47 residues processed: 226 average time/residue: 0.7438 time to fit residues: 181.0731 Evaluate side-chains 235 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 627 ARG Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 27 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.094203 restraints weight = 15381.811| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.50 r_work: 0.2929 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14691 Z= 0.154 Angle : 0.496 9.037 19977 Z= 0.275 Chirality : 0.043 0.134 2172 Planarity : 0.005 0.055 2604 Dihedral : 6.057 58.004 2089 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 4.69 % Allowed : 17.12 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1758 helix: 1.77 (0.30), residues: 300 sheet: 0.68 (0.21), residues: 540 loop : -0.48 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 627 TYR 0.022 0.001 TYR A 655 PHE 0.021 0.002 PHE B 287 TRP 0.010 0.002 TRP B 354 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00361 (14673) covalent geometry : angle 0.49300 (19938) SS BOND : bond 0.00601 ( 15) SS BOND : angle 1.25933 ( 30) hydrogen bonds : bond 0.04882 ( 542) hydrogen bonds : angle 5.07415 ( 1713) link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 1.74282 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 0.514 Fit side-chains REVERT: A 138 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6205 (tt0) REVERT: A 195 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: A 233 GLU cc_start: 0.8018 (tp30) cc_final: 0.7775 (tp30) REVERT: A 320 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8355 (tttt) REVERT: A 415 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7407 (mmtp) REVERT: A 652 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 679 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: B 187 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 195 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 233 GLU cc_start: 0.8117 (tp30) cc_final: 0.7876 (tp30) REVERT: B 320 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8353 (tttt) REVERT: B 415 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7264 (mmtp) REVERT: B 496 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8217 (mmtm) REVERT: B 652 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 661 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7382 (mtp-110) REVERT: C 195 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: C 219 GLU cc_start: 0.8730 (tt0) cc_final: 0.8439 (mm-30) REVERT: C 233 GLU cc_start: 0.8034 (tp30) cc_final: 0.7828 (tp30) REVERT: C 320 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8331 (tttt) REVERT: C 415 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7412 (mptt) REVERT: C 652 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 679 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: C 695 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7592 (tttt) outliers start: 72 outliers final: 49 residues processed: 227 average time/residue: 0.7487 time to fit residues: 182.7775 Evaluate side-chains 234 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 157 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.092642 restraints weight = 15532.303| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.58 r_work: 0.2901 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14691 Z= 0.215 Angle : 0.551 9.535 19977 Z= 0.304 Chirality : 0.046 0.156 2172 Planarity : 0.005 0.065 2604 Dihedral : 6.298 61.604 2089 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.36 % Allowed : 17.45 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1758 helix: 1.60 (0.30), residues: 300 sheet: 0.60 (0.21), residues: 540 loop : -0.53 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 627 TYR 0.023 0.002 TYR A 655 PHE 0.025 0.002 PHE B 287 TRP 0.010 0.002 TRP C 356 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00512 (14673) covalent geometry : angle 0.54698 (19938) SS BOND : bond 0.00783 ( 15) SS BOND : angle 1.61513 ( 30) hydrogen bonds : bond 0.05390 ( 542) hydrogen bonds : angle 5.20526 ( 1713) link_NAG-ASN : bond 0.00361 ( 3) link_NAG-ASN : angle 1.87228 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.557 Fit side-chains REVERT: A 138 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6186 (tt0) REVERT: A 195 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 233 GLU cc_start: 0.8039 (tp30) cc_final: 0.7776 (tp30) REVERT: A 320 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8292 (tttt) REVERT: A 415 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7328 (mmtp) REVERT: A 652 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 679 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: B 138 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6269 (tt0) REVERT: B 187 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: B 195 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 233 GLU cc_start: 0.8140 (tp30) cc_final: 0.7878 (tp30) REVERT: B 320 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8285 (tttt) REVERT: B 415 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7199 (mmtp) REVERT: B 496 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8143 (mmtm) REVERT: B 652 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 661 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7396 (mtp-110) REVERT: C 195 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: C 219 GLU cc_start: 0.8744 (tt0) cc_final: 0.8396 (mm-30) REVERT: C 233 GLU cc_start: 0.8037 (tp30) cc_final: 0.7807 (tp30) REVERT: C 320 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8259 (tttt) REVERT: C 415 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7370 (mptt) REVERT: C 652 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7512 (mm-30) REVERT: C 679 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: C 695 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7502 (tttt) outliers start: 67 outliers final: 50 residues processed: 220 average time/residue: 0.7402 time to fit residues: 175.3720 Evaluate side-chains 235 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.093107 restraints weight = 15335.901| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.60 r_work: 0.2911 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14691 Z= 0.181 Angle : 0.521 9.320 19977 Z= 0.288 Chirality : 0.045 0.153 2172 Planarity : 0.005 0.061 2604 Dihedral : 6.211 60.544 2089 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 4.30 % Allowed : 17.64 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1758 helix: 1.65 (0.30), residues: 300 sheet: 0.63 (0.21), residues: 537 loop : -0.52 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 627 TYR 0.023 0.002 TYR A 655 PHE 0.023 0.002 PHE B 287 TRP 0.009 0.002 TRP C 356 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00428 (14673) covalent geometry : angle 0.51720 (19938) SS BOND : bond 0.00686 ( 15) SS BOND : angle 1.45087 ( 30) hydrogen bonds : bond 0.05112 ( 542) hydrogen bonds : angle 5.14050 ( 1713) link_NAG-ASN : bond 0.00323 ( 3) link_NAG-ASN : angle 1.78181 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 0.577 Fit side-chains REVERT: A 138 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6217 (tt0) REVERT: A 195 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 233 GLU cc_start: 0.8054 (tp30) cc_final: 0.7798 (tp30) REVERT: A 320 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8338 (tttt) REVERT: A 415 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7376 (mmtp) REVERT: A 496 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (mmtm) REVERT: A 652 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 679 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: B 187 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: B 195 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: B 233 GLU cc_start: 0.8163 (tp30) cc_final: 0.7905 (tp30) REVERT: B 320 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8325 (tttt) REVERT: B 415 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7227 (mmtp) REVERT: B 496 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8177 (mmtm) REVERT: B 652 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 661 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7522 (mtt-85) REVERT: C 112 ASN cc_start: 0.7790 (t0) cc_final: 0.7406 (t0) REVERT: C 195 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: C 219 GLU cc_start: 0.8747 (tt0) cc_final: 0.8437 (mm-30) REVERT: C 233 GLU cc_start: 0.8050 (tp30) cc_final: 0.7831 (tp30) REVERT: C 320 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8299 (tttt) REVERT: C 415 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7377 (mptt) REVERT: C 652 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 679 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: C 695 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7547 (tttt) outliers start: 66 outliers final: 51 residues processed: 224 average time/residue: 0.7347 time to fit residues: 177.4596 Evaluate side-chains 237 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 633 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 633 CYS Chi-restraints excluded: chain C residue 639 ARG Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 97 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS A 580 ASN A 620 ASN B 580 ASN B 620 ASN C 580 ASN C 620 ASN C 657 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092980 restraints weight = 15324.655| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.60 r_work: 0.2909 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14691 Z= 0.185 Angle : 0.527 9.378 19977 Z= 0.291 Chirality : 0.045 0.148 2172 Planarity : 0.005 0.059 2604 Dihedral : 6.227 60.434 2089 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.36 % Allowed : 17.90 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1758 helix: 1.64 (0.30), residues: 300 sheet: 0.63 (0.21), residues: 537 loop : -0.52 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 627 TYR 0.024 0.002 TYR B 655 PHE 0.023 0.002 PHE B 287 TRP 0.010 0.002 TRP B 354 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00438 (14673) covalent geometry : angle 0.52299 (19938) SS BOND : bond 0.00697 ( 15) SS BOND : angle 1.48201 ( 30) hydrogen bonds : bond 0.05162 ( 542) hydrogen bonds : angle 5.15237 ( 1713) link_NAG-ASN : bond 0.00330 ( 3) link_NAG-ASN : angle 1.79449 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6899.85 seconds wall clock time: 117 minutes 58.01 seconds (7078.01 seconds total)