Starting phenix.real_space_refine on Mon Apr 6 09:20:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5u_47528/04_2026/9e5u_47528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5u_47528/04_2026/9e5u_47528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e5u_47528/04_2026/9e5u_47528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5u_47528/04_2026/9e5u_47528.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e5u_47528/04_2026/9e5u_47528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5u_47528/04_2026/9e5u_47528.map" } resolution = 2.46 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= 0.050 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 10791 2.51 5 N 2988 2.21 5 O 3174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 17043 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5653 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 31, 'TRANS': 678} Chain breaks: 3 Chain: "B" Number of atoms: 5653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5653 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 31, 'TRANS': 678} Chain breaks: 3 Chain: "C" Number of atoms: 5653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5653 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 31, 'TRANS': 678} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.65, per 1000 atoms: 0.21 Number of scatterers: 17043 At special positions: 0 Unit cell: (120.12, 121.44, 185.46, 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 3174 8.00 N 2988 7.00 C 10791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.04 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG A1002 " - " ASN A 398 " " NAG B1001 " - " ASN B 141 " " NAG B1002 " - " ASN B 398 " " NAG C1001 " - " ASN C 398 " " NAG C1002 " - " ASN C 141 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 731.2 milliseconds 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 32 sheets defined 38.1% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 91 through 106 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 251 through 255 removed outlier: 3.560A pdb=" N TYR A 254 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 255 " --> pdb=" O LEU A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 257 through 266 removed outlier: 3.558A pdb=" N GLY A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 4.482A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (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 removed outlier: 3.953A pdb=" N VAL A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 510 through 546 removed outlier: 4.616A pdb=" N HIS A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 685 through 691 removed outlier: 4.184A 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 739 removed outlier: 4.170A pdb=" N ALA A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 773 removed outlier: 3.816A pdb=" N ASN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 removed outlier: 3.720A pdb=" N SER A 803 " --> pdb=" O MET A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 837 through 859 removed outlier: 4.120A pdb=" N THR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 176 through 181 removed outlier: 4.283A pdb=" N GLN B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) 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 251 through 255 removed outlier: 3.544A pdb=" N TYR B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 255 " --> pdb=" O LEU B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.827A pdb=" N VAL B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 510 through 546 removed outlier: 4.690A pdb=" N HIS B 516 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 685 through 691 removed outlier: 4.175A 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 739 removed outlier: 4.105A pdb=" N ALA B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 773 removed outlier: 3.828A pdb=" N ASN B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 803 removed outlier: 3.713A pdb=" N SER B 803 " --> pdb=" O MET B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'B' and resid 837 through 858 removed outlier: 3.625A pdb=" N MET B 856 " --> pdb=" O LEU B 852 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 176 through 181 removed outlier: 4.280A pdb=" N GLN C 181 " --> pdb=" O HIS C 177 " (cutoff:3.500A) 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 251 through 255 removed outlier: 3.582A pdb=" N TYR C 254 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 255 " --> pdb=" O LEU C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 257 through 266 removed outlier: 3.500A pdb=" N GLY C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.947A pdb=" N VAL C 407 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 429 Processing helix chain 'C' and resid 458 through 467 Processing helix chain 'C' and resid 510 through 546 removed outlier: 4.681A pdb=" N HIS C 516 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 685 through 691 removed outlier: 4.201A 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 739 removed outlier: 4.094A pdb=" N ALA C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 773 removed outlier: 3.831A pdb=" N ASN C 773 " --> pdb=" O SER C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 803 removed outlier: 3.707A pdb=" N SER C 803 " --> pdb=" O MET C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 810 Processing helix chain 'C' and resid 837 through 858 removed outlier: 3.682A pdb=" N MET C 856 " --> pdb=" O LEU C 852 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG C 858 " --> pdb=" O SER C 854 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.058A pdb=" N THR C 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 5.344A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 5.344A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.281A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.681A 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 214 Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB3, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.650A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.495A pdb=" N THR A 665 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB6, first strand: chain 'B' and resid 433 through 435 removed outlier: 3.554A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 443 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN B 398 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 374 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY B 145 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 376 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR B 143 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 191 Processing sheet with id=AB8, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.286A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'B' and resid 210 through 214 Processing sheet with id=AC2, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC3, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.640A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 665 through 667 removed outlier: 6.437A pdb=" N THR B 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.492A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 622 " --> pdb=" O GLY C 618 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 395 through 397 removed outlier: 5.361A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU C 374 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 145 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU C 376 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 143 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.333A 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: 5.361A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU C 374 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 145 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU C 376 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 143 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.285A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.630A 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 214 Processing sheet with id=AD4, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD5, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.671A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2622 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: 3.48 Time building geometry restraints manager: 1.76 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: 5648 1.34 - 1.46: 4317 1.46 - 1.59: 7336 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 17451 Sorted by residual: bond pdb=" C5 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" C5 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" CB MET B 856 " pdb=" CG MET B 856 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB CYS A 529 " pdb=" SG CYS A 529 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.10e+00 ... (remaining 17446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 23507 2.25 - 4.50: 154 4.50 - 6.75: 13 6.75 - 9.00: 3 9.00 - 11.25: 2 Bond angle restraints: 23679 Sorted by residual: angle pdb=" CB MET B 856 " pdb=" CG MET B 856 " pdb=" SD MET B 856 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CB MET C 856 " pdb=" CG MET C 856 " pdb=" SD MET C 856 " ideal model delta sigma weight residual 112.70 122.56 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CA MET C 846 " pdb=" CB MET C 846 " pdb=" CG MET C 846 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.82e+00 angle pdb=" N TYR C 282 " pdb=" CA TYR C 282 " pdb=" C TYR C 282 " ideal model delta sigma weight residual 109.81 116.34 -6.53 2.21e+00 2.05e-01 8.73e+00 angle pdb=" CA MET B 856 " pdb=" CB MET B 856 " pdb=" CG MET B 856 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.88e+00 ... (remaining 23674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 9116 18.19 - 36.38: 970 36.38 - 54.57: 284 54.57 - 72.76: 81 72.76 - 90.95: 22 Dihedral angle restraints: 10473 sinusoidal: 4245 harmonic: 6228 Sorted by residual: 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 -178.38 -88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual -86.00 -172.14 86.14 1 1.00e+01 1.00e-02 8.95e+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 93.00 177.39 -84.39 1 1.00e+01 1.00e-02 8.66e+01 ... (remaining 10470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2519 0.103 - 0.207: 77 0.207 - 0.310: 0 0.310 - 0.413: 1 0.413 - 0.517: 1 Chirality restraints: 2598 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" C1 NAG C1002 " pdb=" ND2 ASN C 141 " pdb=" C2 NAG C1002 " pdb=" O5 NAG C1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C5 NAG C1002 " pdb=" C4 NAG C1002 " pdb=" C6 NAG C1002 " pdb=" O5 NAG C1002 " both_signs ideal model delta sigma weight residual False -2.41 -2.56 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2595 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1002 " -0.279 2.00e-02 2.50e+03 2.38e-01 7.08e+02 pdb=" C7 NAG C1002 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C1002 " -0.170 2.00e-02 2.50e+03 pdb=" N2 NAG C1002 " 0.412 2.00e-02 2.50e+03 pdb=" O7 NAG C1002 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1001 " 0.255 2.00e-02 2.50e+03 2.15e-01 5.80e+02 pdb=" C7 NAG B1001 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B1001 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B1001 " -0.367 2.00e-02 2.50e+03 pdb=" O7 NAG B1001 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 347 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO C 348 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.025 5.00e-02 4.00e+02 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3704 2.79 - 3.32: 14617 3.32 - 3.84: 28485 3.84 - 4.37: 33366 4.37 - 4.90: 57482 Nonbonded interactions: 137654 Sorted by model distance: nonbonded pdb=" OD2 ASP A 720 " pdb=" NH2 ARG B 715 " model vdw 2.262 3.120 nonbonded pdb=" OG SER A 854 " pdb=" OH TYR C 810 " model vdw 2.271 3.040 nonbonded pdb=" NH2 ARG A 715 " pdb=" OD2 ASP C 720 " model vdw 2.273 3.120 nonbonded pdb=" O GLY C 306 " pdb=" OG1 THR C 309 " model vdw 2.277 3.040 nonbonded pdb=" O LEU C 506 " pdb=" OG1 THR C 509 " model vdw 2.282 3.040 ... (remaining 137649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.130 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: 0.560 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.710 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.002 0.035 17472 Z= 0.102 Angle : 0.482 11.248 23727 Z= 0.250 Chirality : 0.041 0.517 2598 Planarity : 0.007 0.238 3078 Dihedral : 17.116 90.947 6426 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.18 % Allowed : 22.87 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.18), residues: 2106 helix: 2.86 (0.19), residues: 714 sheet: 1.18 (0.22), residues: 528 loop : 0.07 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 707 TYR 0.016 0.001 TYR C 282 PHE 0.010 0.001 PHE A 287 TRP 0.007 0.001 TRP B 354 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00214 (17451) covalent geometry : angle 0.47161 (23679) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.99895 ( 30) hydrogen bonds : bond 0.12397 ( 854) hydrogen bonds : angle 6.02938 ( 2622) link_NAG-ASN : bond 0.00313 ( 6) link_NAG-ASN : angle 2.59296 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLN cc_start: 0.8431 (mt0) cc_final: 0.8138 (mt0) REVERT: B 187 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7035 (pp20) REVERT: B 235 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8045 (mmpt) REVERT: B 318 ARG cc_start: 0.7179 (mmp-170) cc_final: 0.6327 (mtp180) REVERT: B 374 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: C 187 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7074 (pp20) REVERT: C 318 ARG cc_start: 0.7212 (mmp-170) cc_final: 0.6509 (mtp85) REVERT: C 360 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6712 (mtp180) outliers start: 39 outliers final: 24 residues processed: 215 average time/residue: 0.6084 time to fit residues: 145.6457 Evaluate side-chains 218 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 845 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 0.3980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 255 ASN B 248 HIS C 140 GLN C 238 ASN C 248 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134772 restraints weight = 17590.525| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.62 r_work: 0.3478 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17472 Z= 0.099 Angle : 0.472 7.374 23727 Z= 0.252 Chirality : 0.040 0.139 2598 Planarity : 0.003 0.046 3078 Dihedral : 6.171 63.430 2570 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.91 % Allowed : 20.97 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.18), residues: 2106 helix: 2.98 (0.19), residues: 717 sheet: 1.20 (0.22), residues: 552 loop : 0.05 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 707 TYR 0.010 0.001 TYR B 282 PHE 0.013 0.001 PHE B 287 TRP 0.007 0.001 TRP B 354 HIS 0.003 0.000 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00198 (17451) covalent geometry : angle 0.46652 (23679) SS BOND : bond 0.00466 ( 15) SS BOND : angle 1.36983 ( 30) hydrogen bonds : bond 0.04429 ( 854) hydrogen bonds : angle 4.55913 ( 2622) link_NAG-ASN : bond 0.00214 ( 6) link_NAG-ASN : angle 2.03367 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.5588 (mpp) REVERT: A 235 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7404 (mtpp) REVERT: A 344 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8769 (mp) REVERT: A 374 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7774 (mm-30) REVERT: A 411 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6865 (t70) REVERT: A 557 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8206 (ptt180) REVERT: B 318 ARG cc_start: 0.7178 (mmp-170) cc_final: 0.6312 (mtp180) REVERT: B 374 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: B 622 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: B 814 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6195 (m) REVERT: C 235 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7813 (mmpt) REVERT: C 318 ARG cc_start: 0.7115 (mmp-170) cc_final: 0.6425 (mtp180) REVERT: C 374 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7376 (mm-30) REVERT: C 421 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8793 (mtm) REVERT: C 622 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8149 (tt0) outliers start: 70 outliers final: 20 residues processed: 241 average time/residue: 0.5679 time to fit residues: 153.2883 Evaluate side-chains 218 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 622 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 102 optimal weight: 0.1980 chunk 48 optimal weight: 0.0670 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 181 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.187818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135684 restraints weight = 17728.218| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.63 r_work: 0.3486 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17472 Z= 0.093 Angle : 0.455 7.257 23727 Z= 0.242 Chirality : 0.040 0.140 2598 Planarity : 0.003 0.045 3078 Dihedral : 5.250 61.052 2531 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.97 % Allowed : 21.25 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.18), residues: 2106 helix: 3.06 (0.19), residues: 717 sheet: 1.15 (0.22), residues: 552 loop : 0.01 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 707 TYR 0.009 0.001 TYR A 282 PHE 0.012 0.001 PHE B 287 TRP 0.007 0.001 TRP B 354 HIS 0.003 0.000 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00189 (17451) covalent geometry : angle 0.44897 (23679) SS BOND : bond 0.00412 ( 15) SS BOND : angle 1.50393 ( 30) hydrogen bonds : bond 0.04155 ( 854) hydrogen bonds : angle 4.30074 ( 2622) link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 1.96778 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 190 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7420 (mtpp) REVERT: A 318 ARG cc_start: 0.7131 (mmp-170) cc_final: 0.6430 (mtp180) REVERT: A 374 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: A 411 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6793 (t70) REVERT: A 557 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8232 (ptt180) REVERT: A 807 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7862 (ttmt) REVERT: B 187 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: B 318 ARG cc_start: 0.7180 (mmp-170) cc_final: 0.6310 (mtp180) REVERT: B 622 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: B 814 THR cc_start: 0.6398 (OUTLIER) cc_final: 0.6176 (m) REVERT: C 187 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: C 235 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7786 (mmpt) REVERT: C 318 ARG cc_start: 0.7093 (mmp-170) cc_final: 0.6444 (mtp180) REVERT: C 344 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8742 (mp) REVERT: C 374 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: C 535 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8118 (tp30) REVERT: C 622 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: C 846 MET cc_start: 0.6772 (tpt) cc_final: 0.6481 (tpt) outliers start: 71 outliers final: 28 residues processed: 247 average time/residue: 0.5638 time to fit residues: 155.8594 Evaluate side-chains 227 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 190 optimal weight: 0.0570 chunk 72 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS C 172 GLN C 248 HIS C 321 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.182927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129211 restraints weight = 17423.420| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.60 r_work: 0.3404 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17472 Z= 0.187 Angle : 0.591 9.773 23727 Z= 0.317 Chirality : 0.044 0.228 2598 Planarity : 0.004 0.046 3078 Dihedral : 5.571 59.015 2526 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.98 % Allowed : 20.25 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2106 helix: 2.74 (0.19), residues: 720 sheet: 1.01 (0.22), residues: 546 loop : -0.12 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 562 TYR 0.013 0.002 TYR C 282 PHE 0.021 0.002 PHE C 287 TRP 0.011 0.001 TRP B 354 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00423 (17451) covalent geometry : angle 0.58152 (23679) SS BOND : bond 0.00942 ( 15) SS BOND : angle 2.60445 ( 30) hydrogen bonds : bond 0.05792 ( 854) hydrogen bonds : angle 4.55492 ( 2622) link_NAG-ASN : bond 0.00059 ( 6) link_NAG-ASN : angle 2.16625 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 191 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7485 (mtpp) REVERT: A 318 ARG cc_start: 0.7254 (mmp-170) cc_final: 0.6472 (mtp180) REVERT: A 344 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8782 (mp) REVERT: A 374 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: A 411 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.7009 (t70) REVERT: A 557 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8246 (ptt180) REVERT: A 622 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: A 807 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7896 (ttmt) REVERT: B 187 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: B 318 ARG cc_start: 0.7251 (mmp-170) cc_final: 0.6400 (mtp180) REVERT: B 337 THR cc_start: 0.5996 (OUTLIER) cc_final: 0.5744 (t) REVERT: B 360 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6471 (mtp180) REVERT: B 374 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: B 434 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8246 (pp) REVERT: B 622 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: B 814 THR cc_start: 0.6500 (OUTLIER) cc_final: 0.6236 (m) REVERT: C 187 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: C 235 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7819 (mmpt) REVERT: C 318 ARG cc_start: 0.7219 (mmp-170) cc_final: 0.6491 (mtp180) REVERT: C 344 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8785 (mp) REVERT: C 349 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8134 (mtpp) REVERT: C 374 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: C 622 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: C 846 MET cc_start: 0.6740 (tpt) cc_final: 0.6447 (tpt) outliers start: 89 outliers final: 42 residues processed: 264 average time/residue: 0.5956 time to fit residues: 175.2260 Evaluate side-chains 246 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 133 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 248 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS C 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129596 restraints weight = 17305.683| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.62 r_work: 0.3412 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17472 Z= 0.154 Angle : 0.556 9.069 23727 Z= 0.297 Chirality : 0.043 0.189 2598 Planarity : 0.004 0.047 3078 Dihedral : 5.537 58.050 2526 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.70 % Allowed : 20.64 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.18), residues: 2106 helix: 2.74 (0.19), residues: 717 sheet: 0.92 (0.21), residues: 549 loop : -0.17 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 466 TYR 0.013 0.002 TYR A 282 PHE 0.019 0.001 PHE B 287 TRP 0.011 0.001 TRP B 354 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00341 (17451) covalent geometry : angle 0.54651 (23679) SS BOND : bond 0.00808 ( 15) SS BOND : angle 2.46564 ( 30) hydrogen bonds : bond 0.05457 ( 854) hydrogen bonds : angle 4.49344 ( 2622) link_NAG-ASN : bond 0.00102 ( 6) link_NAG-ASN : angle 2.09228 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 190 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7443 (mtpp) REVERT: A 318 ARG cc_start: 0.7230 (mmp-170) cc_final: 0.6453 (mtp180) REVERT: A 344 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8756 (mp) REVERT: A 374 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: A 557 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8266 (ptt180) REVERT: A 607 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: A 622 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: B 187 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: B 318 ARG cc_start: 0.7232 (mmp-170) cc_final: 0.6374 (mtp180) REVERT: B 374 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: B 434 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8242 (pp) REVERT: B 622 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: B 814 THR cc_start: 0.6456 (OUTLIER) cc_final: 0.6164 (m) REVERT: C 187 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: C 235 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7830 (mmpt) REVERT: C 318 ARG cc_start: 0.7250 (mmp-170) cc_final: 0.6576 (mtp180) REVERT: C 337 THR cc_start: 0.6117 (OUTLIER) cc_final: 0.5880 (t) REVERT: C 344 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8779 (mp) REVERT: C 374 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: C 587 MET cc_start: 0.9060 (mtp) cc_final: 0.8827 (mtp) REVERT: C 622 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: C 852 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7105 (mm) outliers start: 84 outliers final: 43 residues processed: 259 average time/residue: 0.5978 time to fit residues: 172.5140 Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 850 MET Chi-restraints excluded: chain C residue 852 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 248 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129784 restraints weight = 17341.419| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.61 r_work: 0.3412 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17472 Z= 0.154 Angle : 0.557 9.062 23727 Z= 0.297 Chirality : 0.043 0.183 2598 Planarity : 0.004 0.048 3078 Dihedral : 5.529 57.847 2526 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.75 % Allowed : 20.75 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.18), residues: 2106 helix: 2.70 (0.19), residues: 717 sheet: 0.90 (0.21), residues: 549 loop : -0.20 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 466 TYR 0.013 0.002 TYR C 380 PHE 0.019 0.001 PHE B 287 TRP 0.011 0.001 TRP B 354 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00341 (17451) covalent geometry : angle 0.54652 (23679) SS BOND : bond 0.00774 ( 15) SS BOND : angle 2.55840 ( 30) hydrogen bonds : bond 0.05431 ( 854) hydrogen bonds : angle 4.48004 ( 2622) link_NAG-ASN : bond 0.00093 ( 6) link_NAG-ASN : angle 2.10019 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 187 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7473 (mtpp) REVERT: A 318 ARG cc_start: 0.7271 (mmp-170) cc_final: 0.6478 (mtp180) REVERT: A 344 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8759 (mp) REVERT: A 374 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: A 443 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8650 (mp) REVERT: A 557 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8263 (ptt180) REVERT: A 622 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: A 807 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7890 (ttmt) REVERT: B 187 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: B 235 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8187 (mmtm) REVERT: B 318 ARG cc_start: 0.7240 (mmp-170) cc_final: 0.6371 (mtp180) REVERT: B 337 THR cc_start: 0.5910 (OUTLIER) cc_final: 0.5687 (t) REVERT: B 374 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: B 622 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: B 814 THR cc_start: 0.6488 (OUTLIER) cc_final: 0.6187 (m) REVERT: C 187 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: C 235 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7841 (mmpt) REVERT: C 318 ARG cc_start: 0.7277 (mmp-170) cc_final: 0.6547 (mtp180) REVERT: C 337 THR cc_start: 0.6122 (OUTLIER) cc_final: 0.5895 (t) REVERT: C 344 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8779 (mp) REVERT: C 374 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: C 587 MET cc_start: 0.9077 (mtp) cc_final: 0.8858 (mtp) REVERT: C 622 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: C 806 MET cc_start: 0.6970 (tpt) cc_final: 0.6718 (tpt) REVERT: C 852 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7106 (mm) outliers start: 85 outliers final: 45 residues processed: 258 average time/residue: 0.5773 time to fit residues: 166.5044 Evaluate side-chains 252 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 850 MET Chi-restraints excluded: chain C residue 852 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 139 optimal weight: 0.3980 chunk 200 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 321 GLN B 248 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 248 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.182920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128163 restraints weight = 17324.749| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.62 r_work: 0.3382 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17472 Z= 0.111 Angle : 0.495 8.576 23727 Z= 0.264 Chirality : 0.041 0.142 2598 Planarity : 0.003 0.047 3078 Dihedral : 5.238 54.897 2526 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.97 % Allowed : 21.36 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.18), residues: 2106 helix: 2.83 (0.19), residues: 717 sheet: 1.01 (0.22), residues: 549 loop : -0.14 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 466 TYR 0.013 0.001 TYR A 282 PHE 0.016 0.001 PHE B 287 TRP 0.009 0.001 TRP B 354 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00234 (17451) covalent geometry : angle 0.48651 (23679) SS BOND : bond 0.00548 ( 15) SS BOND : angle 2.18392 ( 30) hydrogen bonds : bond 0.04675 ( 854) hydrogen bonds : angle 4.33097 ( 2622) link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 1.95986 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8204 (p) REVERT: A 235 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7485 (mtpp) REVERT: A 318 ARG cc_start: 0.7210 (mmp-170) cc_final: 0.6476 (mtp180) REVERT: A 374 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: A 557 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8309 (ptt180) REVERT: A 622 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: B 187 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: B 318 ARG cc_start: 0.7164 (mmp-170) cc_final: 0.6311 (mtp180) REVERT: B 337 THR cc_start: 0.5836 (OUTLIER) cc_final: 0.5613 (t) REVERT: B 374 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: B 622 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: B 814 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.6209 (m) REVERT: C 172 GLN cc_start: 0.8277 (mt0) cc_final: 0.7940 (pt0) REVERT: C 187 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: C 235 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7778 (mmpt) REVERT: C 318 ARG cc_start: 0.7168 (mmp-170) cc_final: 0.6432 (mtp180) REVERT: C 337 THR cc_start: 0.5893 (OUTLIER) cc_final: 0.5637 (t) REVERT: C 344 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8757 (mp) REVERT: C 374 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: C 587 MET cc_start: 0.9051 (mtp) cc_final: 0.8842 (mtp) REVERT: C 622 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: C 806 MET cc_start: 0.6976 (tpt) cc_final: 0.6713 (tpt) REVERT: C 852 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7070 (mm) outliers start: 71 outliers final: 38 residues processed: 244 average time/residue: 0.5831 time to fit residues: 158.4606 Evaluate side-chains 240 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 850 MET Chi-restraints excluded: chain C residue 852 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 87 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 4 optimal weight: 0.0980 chunk 176 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.182275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127219 restraints weight = 17318.262| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.63 r_work: 0.3371 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17472 Z= 0.129 Angle : 0.526 9.364 23727 Z= 0.280 Chirality : 0.041 0.157 2598 Planarity : 0.004 0.047 3078 Dihedral : 5.328 56.030 2526 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.80 % Allowed : 21.36 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.18), residues: 2106 helix: 2.77 (0.19), residues: 717 sheet: 0.98 (0.21), residues: 549 loop : -0.16 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 466 TYR 0.012 0.001 TYR B 282 PHE 0.017 0.001 PHE C 287 TRP 0.010 0.001 TRP B 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00283 (17451) covalent geometry : angle 0.51595 (23679) SS BOND : bond 0.00653 ( 15) SS BOND : angle 2.56004 ( 30) hydrogen bonds : bond 0.04948 ( 854) hydrogen bonds : angle 4.36063 ( 2622) link_NAG-ASN : bond 0.00150 ( 6) link_NAG-ASN : angle 2.02269 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7501 (mtpp) REVERT: A 318 ARG cc_start: 0.7262 (mmp-170) cc_final: 0.6500 (mtp180) REVERT: A 374 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: A 557 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8300 (ptt180) REVERT: A 622 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: A 807 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7866 (ttmt) REVERT: B 187 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: B 318 ARG cc_start: 0.7199 (mmp-170) cc_final: 0.6333 (mtp180) REVERT: B 337 THR cc_start: 0.5857 (OUTLIER) cc_final: 0.5628 (t) REVERT: B 374 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: B 622 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: B 814 THR cc_start: 0.6511 (OUTLIER) cc_final: 0.6227 (m) REVERT: C 187 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: C 235 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7780 (mmpt) REVERT: C 318 ARG cc_start: 0.7183 (mmp-170) cc_final: 0.6441 (mtp180) REVERT: C 337 THR cc_start: 0.5929 (OUTLIER) cc_final: 0.5671 (t) REVERT: C 344 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8760 (mp) REVERT: C 374 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: C 587 MET cc_start: 0.9048 (mtp) cc_final: 0.8839 (mtp) REVERT: C 622 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: C 806 MET cc_start: 0.6912 (tpt) cc_final: 0.6626 (tpt) REVERT: C 852 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7070 (mm) outliers start: 68 outliers final: 42 residues processed: 242 average time/residue: 0.5423 time to fit residues: 147.3272 Evaluate side-chains 244 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 202 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 4 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.182507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127571 restraints weight = 17297.243| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.63 r_work: 0.3369 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17472 Z= 0.123 Angle : 0.517 10.661 23727 Z= 0.275 Chirality : 0.041 0.147 2598 Planarity : 0.004 0.047 3078 Dihedral : 5.290 55.820 2526 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.97 % Allowed : 21.31 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2106 helix: 2.75 (0.19), residues: 720 sheet: 1.03 (0.21), residues: 546 loop : -0.15 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.012 0.001 TYR B 380 PHE 0.017 0.001 PHE B 287 TRP 0.010 0.001 TRP B 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00268 (17451) covalent geometry : angle 0.50796 (23679) SS BOND : bond 0.00627 ( 15) SS BOND : angle 2.31740 ( 30) hydrogen bonds : bond 0.04856 ( 854) hydrogen bonds : angle 4.33927 ( 2622) link_NAG-ASN : bond 0.00170 ( 6) link_NAG-ASN : angle 1.97252 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7464 (mtpp) REVERT: A 318 ARG cc_start: 0.7261 (mmp-170) cc_final: 0.6479 (mtp180) REVERT: A 374 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: A 557 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8305 (ptt180) REVERT: A 622 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: A 807 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7858 (ttmt) REVERT: B 187 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: B 318 ARG cc_start: 0.7183 (mmp-170) cc_final: 0.6320 (mtp180) REVERT: B 337 THR cc_start: 0.5840 (OUTLIER) cc_final: 0.5616 (t) REVERT: B 374 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: B 622 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: B 814 THR cc_start: 0.6544 (OUTLIER) cc_final: 0.6263 (m) REVERT: C 187 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: C 235 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7769 (mmpt) REVERT: C 318 ARG cc_start: 0.7178 (mmp-170) cc_final: 0.6419 (mtp180) REVERT: C 337 THR cc_start: 0.5914 (OUTLIER) cc_final: 0.5660 (t) REVERT: C 344 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8757 (mp) REVERT: C 374 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: C 622 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: C 852 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7064 (mm) outliers start: 71 outliers final: 47 residues processed: 244 average time/residue: 0.5535 time to fit residues: 151.4594 Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 248 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.182613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127721 restraints weight = 17306.387| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.63 r_work: 0.3373 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17472 Z= 0.122 Angle : 0.519 11.219 23727 Z= 0.275 Chirality : 0.041 0.147 2598 Planarity : 0.003 0.047 3078 Dihedral : 5.275 55.769 2526 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.86 % Allowed : 21.36 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2106 helix: 2.75 (0.19), residues: 720 sheet: 1.04 (0.21), residues: 546 loop : -0.15 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.013 0.001 TYR B 380 PHE 0.016 0.001 PHE B 287 TRP 0.010 0.001 TRP B 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00264 (17451) covalent geometry : angle 0.51063 (23679) SS BOND : bond 0.00619 ( 15) SS BOND : angle 2.25382 ( 30) hydrogen bonds : bond 0.04834 ( 854) hydrogen bonds : angle 4.33140 ( 2622) link_NAG-ASN : bond 0.00164 ( 6) link_NAG-ASN : angle 1.96779 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 185 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7459 (mtpp) REVERT: A 318 ARG cc_start: 0.7255 (mmp-170) cc_final: 0.6469 (mtp180) REVERT: A 374 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: A 557 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8301 (ptt180) REVERT: A 622 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 807 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7866 (ttmt) REVERT: B 187 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: B 318 ARG cc_start: 0.7190 (mmp-170) cc_final: 0.6326 (mtp180) REVERT: B 337 THR cc_start: 0.5834 (OUTLIER) cc_final: 0.5608 (t) REVERT: B 374 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: B 622 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: B 814 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6256 (m) REVERT: C 187 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: C 235 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7774 (mmpt) REVERT: C 337 THR cc_start: 0.5909 (OUTLIER) cc_final: 0.5651 (t) REVERT: C 344 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8754 (mp) REVERT: C 374 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: C 622 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: C 852 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7066 (mm) outliers start: 69 outliers final: 48 residues processed: 241 average time/residue: 0.5583 time to fit residues: 150.5302 Evaluate side-chains 250 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 185 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 807 LYS Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 852 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 133 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 208 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128061 restraints weight = 17331.577| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.64 r_work: 0.3385 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17472 Z= 0.112 Angle : 0.505 11.207 23727 Z= 0.268 Chirality : 0.041 0.143 2598 Planarity : 0.003 0.047 3078 Dihedral : 5.212 55.247 2526 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.80 % Allowed : 21.64 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.18), residues: 2106 helix: 2.77 (0.19), residues: 720 sheet: 1.05 (0.22), residues: 546 loop : -0.13 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.014 0.001 TYR B 380 PHE 0.015 0.001 PHE B 287 TRP 0.010 0.001 TRP B 354 HIS 0.009 0.001 HIS C 248 Details of bonding type rmsd covalent geometry : bond 0.00240 (17451) covalent geometry : angle 0.49761 (23679) SS BOND : bond 0.00548 ( 15) SS BOND : angle 2.08412 ( 30) hydrogen bonds : bond 0.04657 ( 854) hydrogen bonds : angle 4.29993 ( 2622) link_NAG-ASN : bond 0.00197 ( 6) link_NAG-ASN : angle 1.92432 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8153.39 seconds wall clock time: 138 minutes 48.39 seconds (8328.39 seconds total)