Starting phenix.real_space_refine on Mon Apr 6 07:02:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5x_47530/04_2026/9e5x_47530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5x_47530/04_2026/9e5x_47530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e5x_47530/04_2026/9e5x_47530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5x_47530/04_2026/9e5x_47530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e5x_47530/04_2026/9e5x_47530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5x_47530/04_2026/9e5x_47530.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10278 2.51 5 N 2844 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16233 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5397 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5397 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 5397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5397 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 0.19 Number of scatterers: 16233 At special positions: 0 Unit cell: (122.76, 118.14, 182.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3021 8.00 N 2844 7.00 C 10278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.04 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS C 527 " distance=2.05 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS B 392 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS C 392 " distance=2.07 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.04 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=2.05 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=2.09 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 398 " " NAG B1001 " - " ASN B 398 " " NAG C1001 " - " ASN C 398 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 736.4 milliseconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 33 sheets defined 37.4% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 260 through 265 removed outlier: 4.045A pdb=" N TYR A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.935A pdb=" N GLY A 306 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.736A pdb=" N ASP A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 501 through 546 removed outlier: 3.904A pdb=" N ARG A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 4.136A 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 685 through 691 removed outlier: 4.206A pdb=" N TYR A 689 " --> pdb=" O PRO A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 724 Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.840A pdb=" N GLY A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 772 removed outlier: 3.517A pdb=" N VAL A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 removed outlier: 3.543A pdb=" N SER A 803 " --> pdb=" O MET A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 260 through 265 removed outlier: 4.054A pdb=" N TYR B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.907A pdb=" N GLY B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS B 308 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.731A pdb=" N ASP B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 501 through 546 removed outlier: 3.904A pdb=" N ARG B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE B 526 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 4.156A 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 685 through 691 removed outlier: 4.211A pdb=" N TYR B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 724 Processing helix chain 'B' and resid 726 through 742 removed outlier: 3.884A pdb=" N GLY B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET B 742 " --> pdb=" O PHE B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 772 Processing helix chain 'B' and resid 773 through 803 removed outlier: 3.524A pdb=" N SER B 803 " --> pdb=" O MET B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 265 removed outlier: 4.045A pdb=" N TYR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.913A pdb=" N GLY C 306 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 412 through 428 removed outlier: 3.714A pdb=" N ASP C 416 " --> pdb=" O CYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 501 through 546 removed outlier: 3.908A pdb=" N ARG C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C 526 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 4.148A 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 685 through 691 removed outlier: 4.231A pdb=" N TYR C 689 " --> pdb=" O PRO C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 724 Processing helix chain 'C' and resid 726 through 742 removed outlier: 3.909A pdb=" N GLY C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET C 742 " --> pdb=" O PHE C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 772 Processing helix chain 'C' and resid 773 through 803 removed outlier: 3.539A pdb=" N SER C 803 " --> pdb=" O MET C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 810 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: 6.774A pdb=" N VAL A 124 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL B 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN A 126 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.226A pdb=" N TRP A 369 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS A 151 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU A 371 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A 149 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP A 373 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA A 147 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 13.749A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.226A pdb=" N TRP A 369 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS A 151 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU A 371 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A 149 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP A 373 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA A 147 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 13.749A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.228A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 324 " --> pdb=" O THR A 340 " (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 581 through 583 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.551A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.599A pdb=" N THR A 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB5, first strand: chain 'B' and resid 559 through 563 removed outlier: 3.586A pdb=" N THR C 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.207A pdb=" N TRP B 369 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS B 151 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU B 371 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 149 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP B 373 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA B 147 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 13.778A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.207A pdb=" N TRP B 369 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS B 151 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU B 371 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 149 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP B 373 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA B 147 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 13.778A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 191 Processing sheet with id=AB9, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.236A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (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 581 through 583 Processing sheet with id=AC4, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.547A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC7, first strand: chain 'C' and resid 395 through 397 removed outlier: 6.226A pdb=" N TRP C 369 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LYS C 151 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU C 371 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 149 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP C 373 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA C 147 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 13.769A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 395 through 397 removed outlier: 6.226A pdb=" N TRP C 369 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LYS C 151 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU C 371 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 149 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP C 373 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA C 147 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 13.769A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 185 through 191 Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.245A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD3, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AD5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.578A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 1.82 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: 5378 1.34 - 1.46: 4012 1.46 - 1.58: 7080 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 16614 Sorted by residual: bond pdb=" N GLY C 618 " pdb=" CA GLY C 618 " ideal model delta sigma weight residual 1.442 1.466 -0.024 7.70e-03 1.69e+04 1.01e+01 bond pdb=" N VAL C 555 " pdb=" CA VAL C 555 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.94e+00 bond pdb=" N TYR C 597 " pdb=" CA TYR C 597 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.31e-02 5.83e+03 9.77e+00 bond pdb=" N TYR B 597 " pdb=" CA TYR B 597 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.31e-02 5.83e+03 9.24e+00 bond pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.15e-02 7.56e+03 9.15e+00 ... (remaining 16609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 22267 2.55 - 5.11: 251 5.11 - 7.66: 20 7.66 - 10.22: 0 10.22 - 12.77: 1 Bond angle restraints: 22539 Sorted by residual: angle pdb=" CB MET C 183 " pdb=" CG MET C 183 " pdb=" SD MET C 183 " ideal model delta sigma weight residual 112.70 125.47 -12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C CYS B 527 " pdb=" CA CYS B 527 " pdb=" CB CYS B 527 " ideal model delta sigma weight residual 110.85 117.98 -7.13 1.70e+00 3.46e-01 1.76e+01 angle pdb=" CA VAL B 363 " pdb=" C VAL B 363 " pdb=" O VAL B 363 " ideal model delta sigma weight residual 121.72 117.75 3.97 9.60e-01 1.09e+00 1.71e+01 angle pdb=" N CYS A 392 " pdb=" CA CYS A 392 " pdb=" C CYS A 392 " ideal model delta sigma weight residual 112.41 107.07 5.34 1.30e+00 5.92e-01 1.68e+01 angle pdb=" N CYS B 392 " pdb=" CA CYS B 392 " pdb=" C CYS B 392 " ideal model delta sigma weight residual 112.92 108.13 4.79 1.23e+00 6.61e-01 1.52e+01 ... (remaining 22534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 8650 18.07 - 36.14: 918 36.14 - 54.21: 259 54.21 - 72.28: 52 72.28 - 90.35: 24 Dihedral angle restraints: 9903 sinusoidal: 3960 harmonic: 5943 Sorted by residual: 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 6.95 86.05 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual 93.00 167.89 -74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual 93.00 163.76 -70.76 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 9900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1930 0.050 - 0.100: 431 0.100 - 0.151: 90 0.151 - 0.201: 20 0.201 - 0.251: 4 Chirality restraints: 2475 Sorted by residual: chirality pdb=" CA VAL C 559 " pdb=" N VAL C 559 " pdb=" C VAL C 559 " pdb=" CB VAL C 559 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLU B 631 " pdb=" N GLU B 631 " pdb=" C GLU B 631 " pdb=" CB GLU B 631 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2472 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 181 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C GLN A 181 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 181 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 182 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 558 " 0.264 9.50e-02 1.11e+02 1.19e-01 8.65e+00 pdb=" NE ARG C 558 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 558 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 558 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 558 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 515 " -0.203 9.50e-02 1.11e+02 9.10e-02 5.09e+00 pdb=" NE ARG A 515 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 515 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 515 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 515 " -0.008 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2733 2.77 - 3.30: 13921 3.30 - 3.83: 26720 3.83 - 4.37: 32048 4.37 - 4.90: 55661 Nonbonded interactions: 131083 Sorted by model distance: nonbonded pdb=" OG SER A 244 " pdb=" OE1 GLU A 274 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 690 " pdb=" OE1 GLU C 187 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 244 " pdb=" OE1 GLU C 274 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 244 " pdb=" OE1 GLU B 274 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU A 187 " pdb=" OG1 THR B 690 " model vdw 2.253 3.040 ... (remaining 131078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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: 8.740 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.320 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.004 0.063 16635 Z= 0.251 Angle : 0.667 12.770 22584 Z= 0.416 Chirality : 0.046 0.251 2475 Planarity : 0.006 0.119 2928 Dihedral : 16.397 90.349 6033 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.27 % Allowed : 17.72 % Favored : 79.01 % 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: 1.45 (0.18), residues: 2010 helix: 2.54 (0.20), residues: 657 sheet: 1.20 (0.22), residues: 543 loop : -0.56 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.013 0.002 TYR C 640 PHE 0.016 0.001 PHE C 287 TRP 0.018 0.002 TRP B 369 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00419 (16614) covalent geometry : angle 0.65445 (22539) SS BOND : bond 0.02057 ( 18) SS BOND : angle 3.23002 ( 36) hydrogen bonds : bond 0.14915 ( 814) hydrogen bonds : angle 6.28530 ( 2571) link_NAG-ASN : bond 0.00094 ( 3) link_NAG-ASN : angle 1.40480 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8405 (mptp) REVERT: A 232 MET cc_start: 0.7868 (mtp) cc_final: 0.7412 (mtm) REVERT: A 233 GLU cc_start: 0.7856 (tt0) cc_final: 0.7057 (tp30) REVERT: A 349 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7499 (mmtm) REVERT: A 373 ASP cc_start: 0.8601 (m-30) cc_final: 0.8315 (m-30) REVERT: A 622 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: B 144 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: B 187 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: B 232 MET cc_start: 0.7869 (mtp) cc_final: 0.7361 (mtm) REVERT: B 233 GLU cc_start: 0.7929 (tt0) cc_final: 0.7086 (tp30) REVERT: B 349 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7495 (mmtm) REVERT: B 373 ASP cc_start: 0.8517 (m-30) cc_final: 0.8178 (m-30) REVERT: B 622 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: B 754 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6324 (mpt) REVERT: C 99 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7612 (pm20) REVERT: C 232 MET cc_start: 0.7970 (mtp) cc_final: 0.7472 (mtm) REVERT: C 233 GLU cc_start: 0.7985 (tt0) cc_final: 0.7151 (tp30) REVERT: C 320 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7844 (tttp) REVERT: C 349 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7473 (mmtm) REVERT: C 373 ASP cc_start: 0.8512 (m-30) cc_final: 0.8247 (m-30) REVERT: C 385 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7604 (mtp85) outliers start: 56 outliers final: 26 residues processed: 246 average time/residue: 0.5996 time to fit residues: 162.4519 Evaluate side-chains 215 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 675 ILE Chi-restraints excluded: chain C residue 742 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 126 GLN C 248 HIS C 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.183611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120778 restraints weight = 16132.413| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.78 r_work: 0.3265 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16635 Z= 0.186 Angle : 0.586 8.814 22584 Z= 0.320 Chirality : 0.044 0.206 2475 Planarity : 0.005 0.047 2928 Dihedral : 6.641 59.220 2411 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 5.26 % Allowed : 16.37 % Favored : 78.36 % 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: 1.41 (0.18), residues: 2010 helix: 2.56 (0.20), residues: 669 sheet: 1.11 (0.22), residues: 558 loop : -0.66 (0.19), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 691 TYR 0.016 0.002 TYR C 640 PHE 0.026 0.002 PHE C 770 TRP 0.012 0.002 TRP C 539 HIS 0.003 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00429 (16614) covalent geometry : angle 0.58046 (22539) SS BOND : bond 0.00623 ( 18) SS BOND : angle 2.05547 ( 36) hydrogen bonds : bond 0.05386 ( 814) hydrogen bonds : angle 4.80376 ( 2571) link_NAG-ASN : bond 0.00117 ( 3) link_NAG-ASN : angle 1.18792 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 191 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8445 (mptp) REVERT: A 212 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8321 (mmtt) REVERT: A 232 MET cc_start: 0.7920 (mtp) cc_final: 0.7181 (mtm) REVERT: A 233 GLU cc_start: 0.7902 (tt0) cc_final: 0.7043 (tp30) REVERT: A 349 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7470 (mmtm) REVERT: A 373 ASP cc_start: 0.8584 (m-30) cc_final: 0.8236 (m-30) REVERT: A 374 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7920 (pt0) REVERT: A 518 ASN cc_start: 0.7808 (m-40) cc_final: 0.7514 (m-40) REVERT: A 622 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: A 673 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5760 (mp) REVERT: A 754 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.5901 (mpt) REVERT: B 144 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6791 (tm-30) REVERT: B 232 MET cc_start: 0.7905 (mtp) cc_final: 0.7366 (mtm) REVERT: B 233 GLU cc_start: 0.7957 (tt0) cc_final: 0.7118 (tp30) REVERT: B 349 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7479 (mmtm) REVERT: B 622 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: B 754 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6197 (mpt) REVERT: C 232 MET cc_start: 0.7991 (mtp) cc_final: 0.7433 (mtm) REVERT: C 233 GLU cc_start: 0.8006 (tt0) cc_final: 0.7187 (tp30) REVERT: C 320 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7950 (tttp) REVERT: C 349 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7462 (mmtm) REVERT: C 385 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7566 (mtp85) REVERT: C 412 CYS cc_start: 0.6180 (OUTLIER) cc_final: 0.5957 (t) REVERT: C 754 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6198 (mpt) outliers start: 90 outliers final: 43 residues processed: 258 average time/residue: 0.5360 time to fit residues: 154.1709 Evaluate side-chains 239 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 412 CYS Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122209 restraints weight = 16322.024| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.77 r_work: 0.3285 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16635 Z= 0.132 Angle : 0.523 8.732 22584 Z= 0.284 Chirality : 0.041 0.178 2475 Planarity : 0.004 0.048 2928 Dihedral : 5.965 54.991 2393 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 4.97 % Allowed : 16.61 % Favored : 78.42 % 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: 1.51 (0.18), residues: 2010 helix: 2.68 (0.20), residues: 672 sheet: 1.05 (0.22), residues: 576 loop : -0.59 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 515 TYR 0.013 0.001 TYR C 640 PHE 0.017 0.001 PHE C 287 TRP 0.011 0.001 TRP C 539 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00290 (16614) covalent geometry : angle 0.51657 (22539) SS BOND : bond 0.00460 ( 18) SS BOND : angle 2.04767 ( 36) hydrogen bonds : bond 0.04730 ( 814) hydrogen bonds : angle 4.55518 ( 2571) link_NAG-ASN : bond 0.00125 ( 3) link_NAG-ASN : angle 1.00840 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8409 (mptp) REVERT: A 183 MET cc_start: 0.6545 (mpp) cc_final: 0.6307 (mpp) REVERT: A 232 MET cc_start: 0.7867 (mtp) cc_final: 0.7318 (mtm) REVERT: A 233 GLU cc_start: 0.7901 (tt0) cc_final: 0.7044 (tp30) REVERT: A 349 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7472 (mmtm) REVERT: A 373 ASP cc_start: 0.8600 (m-30) cc_final: 0.8228 (m-30) REVERT: A 518 ASN cc_start: 0.7780 (m-40) cc_final: 0.7419 (m-40) REVERT: A 622 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: A 673 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5709 (mt) REVERT: B 99 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7478 (mp0) REVERT: B 144 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: B 232 MET cc_start: 0.7897 (mtp) cc_final: 0.7317 (mtm) REVERT: B 233 GLU cc_start: 0.7954 (tt0) cc_final: 0.7108 (tp30) REVERT: B 310 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.5877 (mp0) REVERT: B 349 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7473 (mmtm) REVERT: B 622 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: C 227 ASP cc_start: 0.7506 (m-30) cc_final: 0.7254 (m-30) REVERT: C 232 MET cc_start: 0.7980 (mtp) cc_final: 0.7416 (mtm) REVERT: C 233 GLU cc_start: 0.8034 (tt0) cc_final: 0.7225 (tp30) REVERT: C 320 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7935 (tttp) REVERT: C 349 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7476 (mmtm) REVERT: C 385 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7528 (mtp85) REVERT: C 673 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5631 (mt) REVERT: C 704 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8137 (mt-10) REVERT: C 754 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6161 (mpt) outliers start: 85 outliers final: 52 residues processed: 249 average time/residue: 0.5178 time to fit residues: 144.3829 Evaluate side-chains 243 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 532 GLN B 248 HIS B 532 GLN C 248 HIS C 532 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120022 restraints weight = 16240.503| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.77 r_work: 0.3251 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16635 Z= 0.190 Angle : 0.583 9.901 22584 Z= 0.316 Chirality : 0.044 0.193 2475 Planarity : 0.005 0.050 2928 Dihedral : 6.172 55.829 2388 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 5.96 % Allowed : 16.32 % Favored : 77.72 % 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: 1.38 (0.18), residues: 2010 helix: 2.56 (0.20), residues: 672 sheet: 1.05 (0.22), residues: 558 loop : -0.70 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 515 TYR 0.016 0.002 TYR C 640 PHE 0.026 0.002 PHE C 770 TRP 0.012 0.002 TRP C 539 HIS 0.004 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00446 (16614) covalent geometry : angle 0.57643 (22539) SS BOND : bond 0.00635 ( 18) SS BOND : angle 2.25436 ( 36) hydrogen bonds : bond 0.05203 ( 814) hydrogen bonds : angle 4.56705 ( 2571) link_NAG-ASN : bond 0.00030 ( 3) link_NAG-ASN : angle 1.30699 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 183 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7431 (mp0) REVERT: A 144 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: A 158 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8423 (mptp) REVERT: A 183 MET cc_start: 0.6415 (mpp) cc_final: 0.6011 (mpp) REVERT: A 212 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8291 (mmtt) REVERT: A 227 ASP cc_start: 0.7575 (m-30) cc_final: 0.7298 (m-30) REVERT: A 232 MET cc_start: 0.7952 (mtp) cc_final: 0.7340 (mtm) REVERT: A 233 GLU cc_start: 0.7936 (tt0) cc_final: 0.7063 (tp30) REVERT: A 349 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7506 (mmtm) REVERT: A 373 ASP cc_start: 0.8590 (m-30) cc_final: 0.8256 (m-30) REVERT: A 518 ASN cc_start: 0.7736 (m-40) cc_final: 0.7352 (m-40) REVERT: A 622 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: A 673 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5698 (mt) REVERT: A 704 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 99 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7504 (mp0) REVERT: B 144 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: B 204 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7771 (mttm) REVERT: B 232 MET cc_start: 0.7949 (mtp) cc_final: 0.7370 (mtm) REVERT: B 233 GLU cc_start: 0.8019 (tt0) cc_final: 0.7134 (tp30) REVERT: B 310 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: B 349 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7486 (mmtm) REVERT: B 515 ARG cc_start: 0.6312 (ttm110) cc_final: 0.5831 (ttm-80) REVERT: B 622 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: C 212 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8341 (mmtm) REVERT: C 227 ASP cc_start: 0.7509 (m-30) cc_final: 0.7230 (m-30) REVERT: C 232 MET cc_start: 0.8004 (mtp) cc_final: 0.7396 (mtm) REVERT: C 233 GLU cc_start: 0.8031 (tt0) cc_final: 0.7195 (tp30) REVERT: C 320 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7970 (tttp) REVERT: C 349 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7482 (mmtm) REVERT: C 385 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7592 (mtp85) REVERT: C 704 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8195 (mt-10) REVERT: C 754 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6164 (mpt) outliers start: 102 outliers final: 60 residues processed: 260 average time/residue: 0.5256 time to fit residues: 152.8440 Evaluate side-chains 251 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 179 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 144 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 91 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.183438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120730 restraints weight = 16123.382| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.77 r_work: 0.3267 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16635 Z= 0.156 Angle : 0.543 8.423 22584 Z= 0.294 Chirality : 0.042 0.158 2475 Planarity : 0.004 0.050 2928 Dihedral : 6.102 55.868 2388 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 6.02 % Allowed : 16.61 % Favored : 77.37 % 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: 1.43 (0.18), residues: 2010 helix: 2.61 (0.20), residues: 672 sheet: 1.01 (0.21), residues: 576 loop : -0.64 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 515 TYR 0.014 0.001 TYR C 640 PHE 0.019 0.001 PHE C 287 TRP 0.012 0.002 TRP C 539 HIS 0.004 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00358 (16614) covalent geometry : angle 0.53677 (22539) SS BOND : bond 0.00492 ( 18) SS BOND : angle 2.11123 ( 36) hydrogen bonds : bond 0.04810 ( 814) hydrogen bonds : angle 4.44692 ( 2571) link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 1.13519 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 183 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: A 158 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8399 (mptp) REVERT: A 227 ASP cc_start: 0.7569 (m-30) cc_final: 0.7263 (m-30) REVERT: A 232 MET cc_start: 0.7975 (mtp) cc_final: 0.7324 (mtm) REVERT: A 233 GLU cc_start: 0.7947 (tt0) cc_final: 0.7046 (tp30) REVERT: A 349 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7518 (mmtm) REVERT: A 373 ASP cc_start: 0.8572 (m-30) cc_final: 0.8232 (m-30) REVERT: A 515 ARG cc_start: 0.6410 (ttm-80) cc_final: 0.5576 (ttm-80) REVERT: A 518 ASN cc_start: 0.7765 (m-40) cc_final: 0.7358 (m-40) REVERT: A 622 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: A 673 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5732 (mt) REVERT: A 704 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 99 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7537 (mp0) REVERT: B 144 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: B 232 MET cc_start: 0.7951 (mtp) cc_final: 0.7367 (mtm) REVERT: B 233 GLU cc_start: 0.8005 (tt0) cc_final: 0.7274 (tp30) REVERT: B 310 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: B 313 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7961 (t) REVERT: B 349 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7486 (mmtm) REVERT: B 515 ARG cc_start: 0.6264 (ttm110) cc_final: 0.5785 (ttm-80) REVERT: B 622 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8313 (tm-30) REVERT: B 754 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6194 (mpt) REVERT: C 99 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7500 (mp0) REVERT: C 212 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8338 (mmtm) REVERT: C 227 ASP cc_start: 0.7518 (m-30) cc_final: 0.7179 (m-30) REVERT: C 232 MET cc_start: 0.7984 (mtp) cc_final: 0.7387 (mtm) REVERT: C 233 GLU cc_start: 0.8039 (tt0) cc_final: 0.7211 (tp30) REVERT: C 320 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7952 (tttp) REVERT: C 349 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7488 (mmtm) REVERT: C 373 ASP cc_start: 0.8625 (m-30) cc_final: 0.8259 (m-30) REVERT: C 385 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7571 (mtp85) REVERT: C 673 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5666 (mt) REVERT: C 704 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8194 (mt-10) REVERT: C 754 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6126 (mpt) outliers start: 103 outliers final: 66 residues processed: 265 average time/residue: 0.5146 time to fit residues: 152.8268 Evaluate side-chains 260 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 180 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 49 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 123 optimal weight: 0.0070 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.183869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121386 restraints weight = 16191.337| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.75 r_work: 0.3266 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16635 Z= 0.143 Angle : 0.529 7.830 22584 Z= 0.285 Chirality : 0.042 0.152 2475 Planarity : 0.004 0.050 2928 Dihedral : 6.070 56.038 2388 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 5.44 % Allowed : 17.60 % Favored : 76.96 % 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: 1.51 (0.18), residues: 2010 helix: 2.64 (0.20), residues: 672 sheet: 1.12 (0.22), residues: 555 loop : -0.57 (0.19), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 515 TYR 0.013 0.001 TYR C 640 PHE 0.031 0.001 PHE B 770 TRP 0.011 0.001 TRP C 539 HIS 0.004 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00324 (16614) covalent geometry : angle 0.52488 (22539) SS BOND : bond 0.00529 ( 18) SS BOND : angle 1.72011 ( 36) hydrogen bonds : bond 0.04643 ( 814) hydrogen bonds : angle 4.40671 ( 2571) link_NAG-ASN : bond 0.00024 ( 3) link_NAG-ASN : angle 1.15347 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 178 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8410 (mptp) REVERT: A 227 ASP cc_start: 0.7595 (m-30) cc_final: 0.7259 (m-30) REVERT: A 232 MET cc_start: 0.7971 (mtp) cc_final: 0.7318 (mtm) REVERT: A 233 GLU cc_start: 0.7966 (tt0) cc_final: 0.7060 (tp30) REVERT: A 349 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7525 (mmtm) REVERT: A 373 ASP cc_start: 0.8543 (m-30) cc_final: 0.8217 (m-30) REVERT: A 518 ASN cc_start: 0.7770 (m-40) cc_final: 0.7339 (m-40) REVERT: A 673 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5699 (mp) REVERT: A 704 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 99 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7533 (mp0) REVERT: B 232 MET cc_start: 0.7959 (mtp) cc_final: 0.7365 (mtm) REVERT: B 233 GLU cc_start: 0.7990 (tt0) cc_final: 0.7262 (tp30) REVERT: B 310 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: B 313 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7968 (t) REVERT: B 349 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7483 (mmtm) REVERT: B 373 ASP cc_start: 0.8492 (m-30) cc_final: 0.8223 (m-30) REVERT: B 515 ARG cc_start: 0.6278 (ttm110) cc_final: 0.5651 (ttm-80) REVERT: B 622 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: B 754 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6131 (mpt) REVERT: C 212 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8332 (mmtm) REVERT: C 227 ASP cc_start: 0.7497 (m-30) cc_final: 0.7168 (m-30) REVERT: C 232 MET cc_start: 0.7974 (mtp) cc_final: 0.7382 (mtm) REVERT: C 233 GLU cc_start: 0.8048 (tt0) cc_final: 0.7209 (tp30) REVERT: C 320 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7955 (tttp) REVERT: C 349 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7484 (mmtm) REVERT: C 373 ASP cc_start: 0.8621 (m-30) cc_final: 0.8266 (m-30) REVERT: C 385 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7601 (mtp85) REVERT: C 704 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 754 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6128 (mpt) outliers start: 93 outliers final: 68 residues processed: 250 average time/residue: 0.5160 time to fit residues: 144.6778 Evaluate side-chains 251 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 173 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Chi-restraints excluded: chain C residue 782 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 147 optimal weight: 4.9990 chunk 191 optimal weight: 0.1980 chunk 163 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 117 optimal weight: 0.4980 chunk 182 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 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 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121581 restraints weight = 16114.725| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.02 r_work: 0.3232 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16635 Z= 0.171 Angle : 0.573 9.613 22584 Z= 0.309 Chirality : 0.043 0.168 2475 Planarity : 0.005 0.050 2928 Dihedral : 5.783 56.381 2382 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 6.02 % Allowed : 17.19 % Favored : 76.78 % 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: 1.44 (0.18), residues: 2010 helix: 2.61 (0.20), residues: 669 sheet: 1.09 (0.22), residues: 555 loop : -0.63 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 639 TYR 0.015 0.002 TYR C 640 PHE 0.019 0.001 PHE C 287 TRP 0.011 0.002 TRP C 539 HIS 0.004 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00399 (16614) covalent geometry : angle 0.56808 (22539) SS BOND : bond 0.00549 ( 18) SS BOND : angle 1.87506 ( 36) hydrogen bonds : bond 0.04918 ( 814) hydrogen bonds : angle 4.48852 ( 2571) link_NAG-ASN : bond 0.00028 ( 3) link_NAG-ASN : angle 1.27334 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 179 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8379 (mptp) REVERT: A 227 ASP cc_start: 0.7571 (m-30) cc_final: 0.7244 (m-30) REVERT: A 232 MET cc_start: 0.8006 (mtp) cc_final: 0.7318 (mtm) REVERT: A 233 GLU cc_start: 0.7991 (tt0) cc_final: 0.6984 (tp30) REVERT: A 349 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7444 (mmtm) REVERT: A 373 ASP cc_start: 0.8556 (m-30) cc_final: 0.8229 (m-30) REVERT: A 518 ASN cc_start: 0.7700 (m-40) cc_final: 0.7267 (m-40) REVERT: A 671 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7883 (pt) REVERT: A 673 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5719 (mp) REVERT: A 704 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 99 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7431 (mp0) REVERT: B 204 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7715 (mttm) REVERT: B 232 MET cc_start: 0.7997 (mtp) cc_final: 0.7371 (mtm) REVERT: B 233 GLU cc_start: 0.8050 (tt0) cc_final: 0.7233 (tp30) REVERT: B 310 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: B 313 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7932 (t) REVERT: B 349 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7413 (mmtm) REVERT: B 515 ARG cc_start: 0.6241 (ttm110) cc_final: 0.5756 (ttm-80) REVERT: B 622 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: B 754 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.5988 (mpt) REVERT: C 212 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8341 (mmtm) REVERT: C 227 ASP cc_start: 0.7468 (m-30) cc_final: 0.7132 (m-30) REVERT: C 229 GLU cc_start: 0.7459 (tt0) cc_final: 0.7140 (tm-30) REVERT: C 232 MET cc_start: 0.8029 (mtp) cc_final: 0.7402 (mtm) REVERT: C 233 GLU cc_start: 0.8078 (tt0) cc_final: 0.7148 (tp30) REVERT: C 320 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7917 (tttp) REVERT: C 349 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7396 (mmtm) REVERT: C 385 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7600 (mtp85) REVERT: C 673 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5614 (mt) REVERT: C 754 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5973 (mpt) outliers start: 103 outliers final: 74 residues processed: 262 average time/residue: 0.5271 time to fit residues: 154.4588 Evaluate side-chains 260 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 173 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 628 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Chi-restraints excluded: chain C residue 782 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 170 optimal weight: 3.9990 chunk 163 optimal weight: 0.0870 chunk 76 optimal weight: 0.0070 chunk 104 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 101 optimal weight: 0.2980 chunk 110 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.187565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126476 restraints weight = 16389.120| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.74 r_work: 0.3349 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16635 Z= 0.090 Angle : 0.463 10.463 22584 Z= 0.248 Chirality : 0.039 0.126 2475 Planarity : 0.004 0.049 2928 Dihedral : 5.236 55.965 2382 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.98 % Allowed : 20.53 % Favored : 76.49 % 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: 1.75 (0.18), residues: 2010 helix: 2.78 (0.20), residues: 669 sheet: 1.33 (0.22), residues: 549 loop : -0.41 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 515 TYR 0.009 0.001 TYR B 640 PHE 0.030 0.001 PHE C 770 TRP 0.010 0.001 TRP C 539 HIS 0.003 0.000 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00181 (16614) covalent geometry : angle 0.45958 (22539) SS BOND : bond 0.00234 ( 18) SS BOND : angle 1.37029 ( 36) hydrogen bonds : bond 0.03762 ( 814) hydrogen bonds : angle 4.17701 ( 2571) link_NAG-ASN : bond 0.00214 ( 3) link_NAG-ASN : angle 0.87518 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8406 (mptp) REVERT: A 183 MET cc_start: 0.6228 (mpp) cc_final: 0.5913 (mpp) REVERT: A 227 ASP cc_start: 0.7553 (m-30) cc_final: 0.7326 (m-30) REVERT: A 232 MET cc_start: 0.7924 (mtp) cc_final: 0.7263 (mtm) REVERT: A 233 GLU cc_start: 0.7880 (tt0) cc_final: 0.7004 (tp30) REVERT: A 373 ASP cc_start: 0.8519 (m-30) cc_final: 0.8195 (m-30) REVERT: A 515 ARG cc_start: 0.6294 (ttm-80) cc_final: 0.5855 (ttm170) REVERT: A 671 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7734 (pt) REVERT: A 701 ASP cc_start: 0.8432 (p0) cc_final: 0.7845 (p0) REVERT: A 704 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8009 (mt-10) REVERT: B 99 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7515 (mp0) REVERT: B 232 MET cc_start: 0.7972 (mtp) cc_final: 0.7367 (mtm) REVERT: B 233 GLU cc_start: 0.7894 (tt0) cc_final: 0.7162 (tp30) REVERT: B 310 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.5926 (mp0) REVERT: B 313 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7934 (t) REVERT: B 373 ASP cc_start: 0.8393 (m-30) cc_final: 0.8145 (m-30) REVERT: B 515 ARG cc_start: 0.6288 (ttm110) cc_final: 0.5782 (ttm-80) REVERT: B 622 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: C 227 ASP cc_start: 0.7444 (m-30) cc_final: 0.7071 (m-30) REVERT: C 232 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7323 (mtm) REVERT: C 233 GLU cc_start: 0.8004 (tt0) cc_final: 0.7212 (tp30) REVERT: C 313 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7922 (t) REVERT: C 320 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7931 (tttp) REVERT: C 373 ASP cc_start: 0.8552 (m-30) cc_final: 0.8341 (m-30) REVERT: C 385 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7608 (mtp85) REVERT: C 704 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7988 (mt-10) outliers start: 51 outliers final: 25 residues processed: 221 average time/residue: 0.5694 time to fit residues: 140.1006 Evaluate side-chains 209 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 0.0030 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 534 HIS B 248 HIS C 248 HIS C 540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125276 restraints weight = 16275.110| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.09 r_work: 0.3256 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16635 Z= 0.247 Angle : 0.663 12.688 22584 Z= 0.355 Chirality : 0.047 0.214 2475 Planarity : 0.005 0.052 2928 Dihedral : 5.664 56.954 2368 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.51 % Allowed : 20.29 % Favored : 76.20 % 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: 1.41 (0.18), residues: 2010 helix: 2.56 (0.20), residues: 669 sheet: 1.17 (0.22), residues: 537 loop : -0.67 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 639 TYR 0.016 0.002 TYR C 640 PHE 0.022 0.002 PHE C 287 TRP 0.012 0.002 TRP B 369 HIS 0.004 0.001 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00591 (16614) covalent geometry : angle 0.65764 (22539) SS BOND : bond 0.00749 ( 18) SS BOND : angle 2.12213 ( 36) hydrogen bonds : bond 0.05461 ( 814) hydrogen bonds : angle 4.56915 ( 2571) link_NAG-ASN : bond 0.00145 ( 3) link_NAG-ASN : angle 1.59429 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8451 (mptm) REVERT: A 183 MET cc_start: 0.6413 (mpp) cc_final: 0.6079 (mpp) REVERT: A 227 ASP cc_start: 0.7583 (m-30) cc_final: 0.7256 (m-30) REVERT: A 232 MET cc_start: 0.8070 (mtp) cc_final: 0.7391 (mtm) REVERT: A 233 GLU cc_start: 0.7967 (tt0) cc_final: 0.7057 (tp30) REVERT: A 373 ASP cc_start: 0.8616 (m-30) cc_final: 0.8311 (m-30) REVERT: A 704 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8280 (mt-10) REVERT: B 99 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7616 (mp0) REVERT: B 232 MET cc_start: 0.8056 (mtp) cc_final: 0.7448 (mtm) REVERT: B 233 GLU cc_start: 0.8004 (tt0) cc_final: 0.7310 (tp30) REVERT: B 310 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: B 313 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7985 (t) REVERT: B 515 ARG cc_start: 0.6394 (ttm110) cc_final: 0.5894 (ttm-80) REVERT: B 622 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: B 754 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6079 (mpt) REVERT: C 227 ASP cc_start: 0.7570 (m-30) cc_final: 0.7264 (m-30) REVERT: C 232 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7443 (mtm) REVERT: C 233 GLU cc_start: 0.8038 (tt0) cc_final: 0.7241 (tp30) REVERT: C 320 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7950 (tttp) REVERT: C 385 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7665 (mtp85) REVERT: C 754 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6213 (mpt) outliers start: 60 outliers final: 43 residues processed: 224 average time/residue: 0.5218 time to fit residues: 131.1074 Evaluate side-chains 223 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 LYS 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 387 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Chi-restraints excluded: chain C residue 782 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 534 HIS B 248 HIS C 248 HIS C 540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122899 restraints weight = 16289.015| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.73 r_work: 0.3303 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16635 Z= 0.131 Angle : 0.544 13.452 22584 Z= 0.291 Chirality : 0.041 0.195 2475 Planarity : 0.004 0.051 2928 Dihedral : 5.422 56.933 2368 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.81 % Allowed : 21.11 % Favored : 76.08 % 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: 1.53 (0.18), residues: 2010 helix: 2.64 (0.20), residues: 669 sheet: 1.14 (0.22), residues: 555 loop : -0.55 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 515 TYR 0.012 0.001 TYR C 640 PHE 0.032 0.001 PHE C 770 TRP 0.010 0.001 TRP B 528 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00293 (16614) covalent geometry : angle 0.54023 (22539) SS BOND : bond 0.00391 ( 18) SS BOND : angle 1.53340 ( 36) hydrogen bonds : bond 0.04519 ( 814) hydrogen bonds : angle 4.38349 ( 2571) link_NAG-ASN : bond 0.00094 ( 3) link_NAG-ASN : angle 1.08360 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8406 (mptp) REVERT: A 183 MET cc_start: 0.6280 (mpp) cc_final: 0.5952 (mpp) REVERT: A 227 ASP cc_start: 0.7542 (m-30) cc_final: 0.7240 (m-30) REVERT: A 232 MET cc_start: 0.8001 (mtp) cc_final: 0.7313 (mtm) REVERT: A 233 GLU cc_start: 0.7938 (tt0) cc_final: 0.7069 (tp30) REVERT: A 373 ASP cc_start: 0.8564 (m-30) cc_final: 0.8243 (m-30) REVERT: A 515 ARG cc_start: 0.6371 (ttm-80) cc_final: 0.5487 (ttm-80) REVERT: A 704 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8244 (mt-10) REVERT: B 99 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7566 (mp0) REVERT: B 232 MET cc_start: 0.8014 (mtp) cc_final: 0.7408 (mtm) REVERT: B 233 GLU cc_start: 0.7954 (tt0) cc_final: 0.7303 (tp30) REVERT: B 310 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: B 313 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7973 (t) REVERT: B 373 ASP cc_start: 0.8529 (m-30) cc_final: 0.8249 (m-30) REVERT: B 515 ARG cc_start: 0.6378 (ttm110) cc_final: 0.5874 (ttm-80) REVERT: B 622 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: C 212 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8306 (mmtm) REVERT: C 227 ASP cc_start: 0.7502 (m-30) cc_final: 0.7131 (m-30) REVERT: C 232 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7419 (mtm) REVERT: C 233 GLU cc_start: 0.8018 (tt0) cc_final: 0.7218 (tp30) REVERT: C 320 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7948 (tttp) REVERT: C 373 ASP cc_start: 0.8604 (m-30) cc_final: 0.8300 (m-30) REVERT: C 385 ARG cc_start: 0.7906 (mmm160) cc_final: 0.7643 (mtp85) REVERT: C 704 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 754 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6266 (mpt) outliers start: 48 outliers final: 33 residues processed: 208 average time/residue: 0.5552 time to fit residues: 128.7318 Evaluate side-chains 208 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 LYS 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 503 PHE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 127 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS C 248 HIS C 540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127485 restraints weight = 16236.620| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.02 r_work: 0.3289 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16635 Z= 0.113 Angle : 0.514 10.970 22584 Z= 0.275 Chirality : 0.040 0.137 2475 Planarity : 0.004 0.050 2928 Dihedral : 5.237 58.886 2368 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.87 % Allowed : 20.99 % Favored : 76.14 % 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: 1.60 (0.18), residues: 2010 helix: 2.70 (0.20), residues: 666 sheet: 1.18 (0.22), residues: 555 loop : -0.48 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 515 TYR 0.012 0.001 TYR C 640 PHE 0.016 0.001 PHE C 287 TRP 0.011 0.001 TRP C 528 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00249 (16614) covalent geometry : angle 0.51135 (22539) SS BOND : bond 0.00326 ( 18) SS BOND : angle 1.42241 ( 36) hydrogen bonds : bond 0.04167 ( 814) hydrogen bonds : angle 4.23214 ( 2571) link_NAG-ASN : bond 0.00090 ( 3) link_NAG-ASN : angle 1.10363 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8088.94 seconds wall clock time: 137 minutes 33.48 seconds (8253.48 seconds total)