Starting phenix.real_space_refine on Sun Sep 13 03:00:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x5b_22048/09_2026/6x5b_22048.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 108 5.16 5 C 12723 2.51 5 N 3456 2.21 5 O 3945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20232 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2769 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Chain breaks: 5 Chain: "B" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "P" 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 chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UOV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, J, E, K, F, M, G, N, I, O, R, T, S, U Time building chain proxies: 4.39, per 1000 atoms: 0.22 Number of scatterers: 20232 At special positions: 0 Unit cell: (150.65, 156.4, 140.3, 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 108 16.00 O 3945 8.00 N 3456 7.00 C 12723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.08 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.08 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.08 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.07 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.07 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.02 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN S 4 " - " MAN S 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 362 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 392 " " NAG A 613 " - " ASN A 413 " " NAG A 614 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG D 607 " - " ASN D 276 " " NAG D 608 " - " ASN D 295 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 362 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 392 " " NAG D 613 " - " ASN D 413 " " NAG D 614 " - " ASN D 448 " " NAG E 701 " - " ASN E 611 " " NAG J 607 " - " ASN J 276 " " NAG J 608 " - " ASN J 295 " " NAG J 609 " - " ASN J 332 " " NAG J 610 " - " ASN J 362 " " NAG J 611 " - " ASN J 386 " " NAG J 612 " - " ASN J 392 " " NAG J 613 " - " ASN J 413 " " NAG J 614 " - " ASN J 448 " " NAG K 701 " - " ASN K 611 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN D 241 " " NAG S 1 " - " ASN D 262 " " NAG T 1 " - " ASN J 241 " " NAG U 1 " - " ASN J 262 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.0% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 65 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.730A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.929A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.843A pdb=" N PHE B 522 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 561 through 564 Processing helix chain 'B' and resid 565 through 593 removed outlier: 3.995A pdb=" N TRP B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.703A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.142A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.461A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 334 through 353 removed outlier: 3.729A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.929A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.843A pdb=" N PHE E 522 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 528 Processing helix chain 'E' and resid 529 through 546 Processing helix chain 'E' and resid 561 through 564 Processing helix chain 'E' and resid 565 through 593 removed outlier: 3.995A pdb=" N TRP E 571 " --> pdb=" O GLN E 567 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 591 " --> pdb=" O LEU E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.702A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 4.142A pdb=" N LYS E 633 " --> pdb=" O MET E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 658 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.461A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'J' and resid 65 through 68 Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 99 through 114 Processing helix chain 'J' and resid 334 through 353 removed outlier: 3.729A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 475 through 484 removed outlier: 3.928A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 516 through 524 removed outlier: 3.843A pdb=" N PHE K 522 " --> pdb=" O PHE K 518 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY K 524 " --> pdb=" O LEU K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 528 Processing helix chain 'K' and resid 529 through 546 Processing helix chain 'K' and resid 561 through 564 Processing helix chain 'K' and resid 565 through 593 removed outlier: 3.995A pdb=" N TRP K 571 " --> pdb=" O GLN K 567 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN K 591 " --> pdb=" O LEU K 587 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 597 Processing helix chain 'K' and resid 618 through 626 removed outlier: 3.703A pdb=" N MET K 626 " --> pdb=" O ILE K 622 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 635 removed outlier: 4.142A pdb=" N LYS K 633 " --> pdb=" O MET K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 658 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 58 through 64 removed outlier: 4.462A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 79 Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 99 through 100C Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.337A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.643A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.838A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.656A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.656A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.767A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 37 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS C 35 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 38 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.337A pdb=" N VAL E 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL D 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR E 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR D 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS E 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AC1, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'D' and resid 199 through 202 Processing sheet with id=AC3, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.643A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.838A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.767A pdb=" N PHE G 26 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 37 " --> pdb=" O TRP G 28 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN G 30 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS G 35 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY G 38 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 12 through 17 Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL I 56 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.337A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 56 Processing sheet with id=AD7, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'J' and resid 199 through 202 Processing sheet with id=AD9, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.642A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 271 through 273 removed outlier: 6.838A pdb=" N THR J 450 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN J 448 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N VAL J 292 " --> pdb=" O SER J 446 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N SER J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 45 through 49 removed outlier: 6.657A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 2 through 5 removed outlier: 4.766A pdb=" N PHE N 26 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU N 37 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN N 30 " --> pdb=" O LYS N 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS N 35 " --> pdb=" O ASN N 30 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY N 38 " --> pdb=" O THR N 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 12 through 17 Processing sheet with id=AE7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.270A pdb=" N GLU O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2142 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: 4.31 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3689 1.31 - 1.45: 6397 1.45 - 1.59: 10290 1.59 - 1.73: 120 1.73 - 1.86: 141 Bond restraints: 20637 Sorted by residual: bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.82e+01 bond pdb=" NE ARG D 504 " pdb=" CZ ARG D 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.77e+01 bond pdb=" NE ARG J 504 " pdb=" CZ ARG J 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.74e+01 bond pdb=" CG HIS D 374 " pdb=" CD2 HIS D 374 " ideal model delta sigma weight residual 1.354 1.283 0.071 1.10e-02 8.26e+03 4.15e+01 bond pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 1.354 1.283 0.071 1.10e-02 8.26e+03 4.11e+01 ... (remaining 20632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 24488 2.56 - 5.13: 3072 5.13 - 7.69: 411 7.69 - 10.25: 13 10.25 - 12.81: 12 Bond angle restraints: 27996 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 119.78 127.40 -7.62 1.03e+00 9.43e-01 5.47e+01 angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 119.78 127.38 -7.60 1.03e+00 9.43e-01 5.44e+01 angle pdb=" N VAL J 65 " pdb=" CA VAL J 65 " pdb=" C VAL J 65 " ideal model delta sigma weight residual 110.42 117.48 -7.06 9.60e-01 1.09e+00 5.41e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.78 127.35 -7.57 1.03e+00 9.43e-01 5.41e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 110.42 117.47 -7.05 9.60e-01 1.09e+00 5.39e+01 ... (remaining 27991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 11508 16.03 - 32.07: 360 32.07 - 48.10: 84 48.10 - 64.14: 75 64.14 - 80.17: 12 Dihedral angle restraints: 12039 sinusoidal: 4896 harmonic: 7143 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.17 80.17 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.16 80.16 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -166.13 80.13 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 12036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2230 0.104 - 0.207: 757 0.207 - 0.311: 142 0.311 - 0.414: 90 0.414 - 0.518: 42 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 3258 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 611 " -0.095 2.00e-02 2.50e+03 9.97e-02 1.24e+02 pdb=" CG ASN K 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN K 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN K 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG K 701 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " -0.095 2.00e-02 2.50e+03 9.97e-02 1.24e+02 pdb=" CG ASN E 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.095 2.00e-02 2.50e+03 9.96e-02 1.24e+02 pdb=" CG ASN B 611 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.155 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.121 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 8756 2.93 - 3.42: 18180 3.42 - 3.91: 34904 3.91 - 4.41: 39609 4.41 - 4.90: 63665 Nonbonded interactions: 165114 Sorted by model distance: nonbonded pdb=" N ASN D 301 " pdb=" N ASN D 302 " model vdw 2.434 2.560 nonbonded pdb=" N ASN A 301 " pdb=" N ASN A 302 " model vdw 2.435 2.560 nonbonded pdb=" N ASN J 301 " pdb=" N ASN J 302 " model vdw 2.435 2.560 nonbonded pdb=" N ASN G 39 " pdb=" OD1 ASN G 39 " model vdw 2.446 3.120 nonbonded pdb=" N ASN C 39 " pdb=" OD1 ASN C 39 " model vdw 2.446 3.120 ... (remaining 165109 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } 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 group one per residue 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: 1.920 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.022 0.122 20718 Z= 1.127 Angle : 1.761 12.814 28206 Z= 1.137 Chirality : 0.126 0.518 3261 Planarity : 0.009 0.055 3519 Dihedral : 10.052 79.536 7326 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2427 helix: -0.36 (0.22), residues: 444 sheet: 0.77 (0.20), residues: 687 loop : 0.48 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 59 TYR 0.068 0.010 TYR F 91 PHE 0.029 0.007 PHE K 522 TRP 0.049 0.010 TRP N 28 HIS 0.008 0.002 HIS J 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02125 / 1.11 (20637) covalent geometry : angle 1.74615 / 1.14 (27996) SS BOND : bond 0.02011 / 1.24 ( 33) SS BOND : angle 2.73696 / 1.98 ( 66) hydrogen bonds : bond 0.15974 / 10.48 ( 807) hydrogen bonds : angle 7.78402 / 5.50 ( 2142) link_ALPHA1-2 : bond 0.07306 / 3.66 ( 3) link_ALPHA1-2 : angle 4.48488 / 2.00 ( 9) link_ALPHA1-3 : bond 0.05282 / 2.65 ( 3) link_ALPHA1-3 : angle 2.31705 / 1.05 ( 9) link_BETA1-4 : bond 0.06762 / 3.30 ( 9) link_BETA1-4 : angle 5.11325 / 2.75 ( 27) link_NAG-ASN : bond 0.08252 / 4.86 ( 33) link_NAG-ASN : angle 2.67976 / 1.77 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 GLN cc_start: 0.7463 (mp10) cc_final: 0.6900 (mt0) REVERT: A 446 SER cc_start: 0.8579 (m) cc_final: 0.8068 (p) REVERT: A 475 MET cc_start: 0.7946 (mmp) cc_final: 0.7641 (tpp) REVERT: B 638 TYR cc_start: 0.7099 (m-80) cc_final: 0.6886 (m-10) REVERT: L 52 SER cc_start: 0.7491 (p) cc_final: 0.7276 (t) REVERT: C 74 LEU cc_start: 0.7327 (tp) cc_final: 0.6418 (tp) REVERT: H 81 GLU cc_start: 0.6204 (tt0) cc_final: 0.5925 (tt0) REVERT: H 111 VAL cc_start: 0.5893 (t) cc_final: 0.5353 (t) REVERT: D 446 SER cc_start: 0.8450 (m) cc_final: 0.7985 (p) REVERT: E 638 TYR cc_start: 0.6894 (m-80) cc_final: 0.6656 (m-10) REVERT: G 74 LEU cc_start: 0.7418 (tp) cc_final: 0.6624 (tp) REVERT: G 86 VAL cc_start: 0.8044 (t) cc_final: 0.7641 (t) REVERT: I 12 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7108 (mmtt) REVERT: I 36 TRP cc_start: 0.7482 (m100) cc_final: 0.7120 (m100) REVERT: I 111 VAL cc_start: 0.6246 (t) cc_final: 0.5470 (t) REVERT: J 116 LEU cc_start: 0.8745 (mt) cc_final: 0.8518 (mp) REVERT: J 428 GLN cc_start: 0.7638 (mp10) cc_final: 0.7173 (mt0) REVERT: J 446 SER cc_start: 0.8556 (m) cc_final: 0.8232 (p) REVERT: J 475 MET cc_start: 0.7925 (mmp) cc_final: 0.7710 (mmm) REVERT: J 482 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6579 (mm-30) REVERT: K 627 THR cc_start: 0.8250 (p) cc_final: 0.7937 (p) REVERT: K 629 MET cc_start: 0.7935 (mmm) cc_final: 0.7625 (mmm) REVERT: K 638 TYR cc_start: 0.6863 (m-80) cc_final: 0.6579 (m-10) REVERT: O 108 LEU cc_start: 0.8688 (tp) cc_final: 0.8474 (tt) REVERT: O 111 VAL cc_start: 0.6308 (t) cc_final: 0.5384 (t) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 0.1550 time to fit residues: 164.5072 Evaluate side-chains 358 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN A 249 HIS A 355 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN L 42 GLN L 93 ASN C 33 GLN C 94 GLN H 58 HIS H 62 HIS D 72 HIS ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 229 ASN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN E 554 ASN E 607 ASN E 620 ASN F 93 ASN I 58 HIS ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 ASN J 249 HIS J 363 HIS J 374 HIS K 564 HIS K 620 ASN O 58 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.169552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.143244 restraints weight = 33252.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.145940 restraints weight = 17651.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.147218 restraints weight = 10198.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.147817 restraints weight = 9031.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.148046 restraints weight = 7911.736| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20718 Z= 0.212 Angle : 0.804 13.155 28206 Z= 0.414 Chirality : 0.050 0.213 3261 Planarity : 0.005 0.048 3519 Dihedral : 5.157 22.140 2688 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.70 % Allowed : 9.50 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2427 helix: 0.70 (0.25), residues: 456 sheet: 0.85 (0.22), residues: 594 loop : 0.00 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 50 TYR 0.029 0.003 TYR A 435 PHE 0.020 0.002 PHE A 53 TRP 0.027 0.002 TRP F 94 HIS 0.008 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (20637) covalent geometry : angle 0.78474 / 0.41 (27996) SS BOND : bond 0.00693 / 0.46 ( 33) SS BOND : angle 1.10172 / 0.80 ( 66) hydrogen bonds : bond 0.05275 / 3.48 ( 807) hydrogen bonds : angle 5.92282 / 4.23 ( 2142) link_ALPHA1-2 : bond 0.00182 / 0.09 ( 3) link_ALPHA1-2 : angle 2.15722 / 1.08 ( 9) link_ALPHA1-3 : bond 0.00803 / 0.41 ( 3) link_ALPHA1-3 : angle 1.63986 / 0.86 ( 9) link_BETA1-4 : bond 0.00240 / 0.12 ( 9) link_BETA1-4 : angle 3.01079 / 1.66 ( 27) link_NAG-ASN : bond 0.00472 / 0.30 ( 33) link_NAG-ASN : angle 2.49770 / 1.65 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 410 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7595 (tm-30) cc_final: 0.6758 (tt0) REVERT: A 426 MET cc_start: 0.7697 (mtp) cc_final: 0.7392 (mtp) REVERT: A 428 GLN cc_start: 0.8250 (mp10) cc_final: 0.7819 (mt0) REVERT: A 446 SER cc_start: 0.8763 (m) cc_final: 0.8042 (p) REVERT: L 2 LEU cc_start: 0.5488 (OUTLIER) cc_final: 0.4853 (mt) REVERT: C 74 LEU cc_start: 0.7011 (tp) cc_final: 0.6803 (tp) REVERT: C 86 VAL cc_start: 0.8310 (t) cc_final: 0.8058 (p) REVERT: H 3 GLN cc_start: 0.8315 (pm20) cc_final: 0.8033 (pm20) REVERT: D 64 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6699 (tt0) REVERT: D 426 MET cc_start: 0.7884 (mtp) cc_final: 0.7539 (mtm) REVERT: D 446 SER cc_start: 0.8690 (m) cc_final: 0.7915 (p) REVERT: E 565 MET cc_start: 0.6721 (ptm) cc_final: 0.6252 (ptm) REVERT: E 638 TYR cc_start: 0.6778 (m-80) cc_final: 0.6567 (m-10) REVERT: F 2 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4508 (mt) REVERT: F 70 GLU cc_start: 0.6743 (mp0) cc_final: 0.6483 (mp0) REVERT: F 79 GLN cc_start: 0.8212 (mm110) cc_final: 0.7983 (mm-40) REVERT: G 58 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7356 (ttt90) REVERT: I 12 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6651 (mmtt) REVERT: J 64 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6646 (tt0) REVERT: J 428 GLN cc_start: 0.8166 (mp10) cc_final: 0.7629 (mt0) REVERT: J 435 TYR cc_start: 0.7951 (m-80) cc_final: 0.7693 (m-10) REVERT: J 446 SER cc_start: 0.8836 (m) cc_final: 0.8346 (p) REVERT: M 24 ARG cc_start: 0.6963 (ttm110) cc_final: 0.6673 (ttm-80) REVERT: N 58 ARG cc_start: 0.8247 (mtp85) cc_final: 0.8019 (ttt90) REVERT: N 71 ILE cc_start: 0.7531 (mt) cc_final: 0.7220 (tt) REVERT: N 86 VAL cc_start: 0.8018 (t) cc_final: 0.7708 (p) REVERT: O 12 LYS cc_start: 0.6745 (mptt) cc_final: 0.5188 (mttp) outliers start: 58 outliers final: 30 residues processed: 444 average time/residue: 0.1505 time to fit residues: 102.7653 Evaluate side-chains 355 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 323 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 79 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 217 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN F 42 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 620 ASN M 42 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.163672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.136170 restraints weight = 33851.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.138982 restraints weight = 18161.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.141301 restraints weight = 10743.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.142014 restraints weight = 8309.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.142044 restraints weight = 7319.620| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20718 Z= 0.227 Angle : 0.749 9.496 28206 Z= 0.383 Chirality : 0.049 0.201 3261 Planarity : 0.005 0.061 3519 Dihedral : 5.218 19.580 2688 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.98 % Allowed : 12.43 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2427 helix: 0.75 (0.25), residues: 441 sheet: 0.62 (0.23), residues: 570 loop : -0.57 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 50 TYR 0.026 0.003 TYR I 100E PHE 0.017 0.002 PHE D 376 TRP 0.036 0.002 TRP H 36 HIS 0.006 0.002 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (20637) covalent geometry : angle 0.73119 / 0.38 (27996) SS BOND : bond 0.00504 / 0.34 ( 33) SS BOND : angle 1.45444 / 1.06 ( 66) hydrogen bonds : bond 0.04923 / 3.22 ( 807) hydrogen bonds : angle 5.80178 / 4.13 ( 2142) link_ALPHA1-2 : bond 0.00730 / 0.36 ( 3) link_ALPHA1-2 : angle 2.42516 / 1.25 ( 9) link_ALPHA1-3 : bond 0.00765 / 0.38 ( 3) link_ALPHA1-3 : angle 1.63531 / 0.87 ( 9) link_BETA1-4 : bond 0.00401 / 0.17 ( 9) link_BETA1-4 : angle 2.67697 / 1.50 ( 27) link_NAG-ASN : bond 0.00272 / 0.17 ( 33) link_NAG-ASN : angle 2.14586 / 1.43 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 381 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7893 (tm-30) cc_final: 0.6991 (tt0) REVERT: A 434 MET cc_start: 0.7450 (ttp) cc_final: 0.7204 (tmm) REVERT: L 24 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6990 (ttm-80) REVERT: L 70 GLU cc_start: 0.6601 (mp0) cc_final: 0.6347 (mp0) REVERT: C 80 ASP cc_start: 0.5980 (m-30) cc_final: 0.5478 (t70) REVERT: C 94 GLN cc_start: 0.7055 (tp40) cc_final: 0.5946 (tp-100) REVERT: H 3 GLN cc_start: 0.8321 (pm20) cc_final: 0.8053 (pm20) REVERT: H 19 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7627 (tmtt) REVERT: H 97 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7456 (mm-30) REVERT: H 108 LEU cc_start: 0.8395 (pp) cc_final: 0.8181 (tt) REVERT: D 64 GLU cc_start: 0.7784 (tm-30) cc_final: 0.6915 (tt0) REVERT: D 446 SER cc_start: 0.8983 (m) cc_final: 0.8217 (p) REVERT: F 70 GLU cc_start: 0.6764 (mp0) cc_final: 0.6376 (mp0) REVERT: I 19 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6560 (tptp) REVERT: J 64 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6645 (tt0) REVERT: J 345 ILE cc_start: 0.7570 (mt) cc_final: 0.7351 (mp) REVERT: J 435 TYR cc_start: 0.7998 (m-80) cc_final: 0.7608 (m-10) REVERT: K 615 SER cc_start: 0.9142 (t) cc_final: 0.8923 (m) REVERT: M 24 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6793 (ttm-80) REVERT: N 58 ARG cc_start: 0.8340 (mtp85) cc_final: 0.8089 (ttt90) REVERT: N 74 LEU cc_start: 0.6685 (tp) cc_final: 0.6168 (tp) REVERT: O 18 VAL cc_start: 0.7999 (t) cc_final: 0.7360 (m) REVERT: O 46 GLU cc_start: 0.6830 (pt0) cc_final: 0.6030 (tp30) REVERT: O 100 ASP cc_start: 0.8114 (m-30) cc_final: 0.7870 (m-30) REVERT: O 108 LEU cc_start: 0.8113 (pp) cc_final: 0.7898 (tt) outliers start: 64 outliers final: 44 residues processed: 414 average time/residue: 0.1368 time to fit residues: 89.6407 Evaluate side-chains 356 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 311 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 237 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN E 653 GLN F 42 GLN J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.161714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.134891 restraints weight = 33849.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.138108 restraints weight = 17487.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.139580 restraints weight = 10166.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.140006 restraints weight = 8725.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.140315 restraints weight = 7668.830| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20718 Z= 0.212 Angle : 0.708 8.213 28206 Z= 0.362 Chirality : 0.048 0.176 3261 Planarity : 0.005 0.060 3519 Dihedral : 5.159 17.614 2688 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.05 % Allowed : 13.18 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2427 helix: 0.98 (0.25), residues: 423 sheet: 0.80 (0.23), residues: 546 loop : -0.83 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 31 TYR 0.032 0.002 TYR M 49 PHE 0.017 0.002 PHE J 53 TRP 0.021 0.002 TRP H 36 HIS 0.005 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (20637) covalent geometry : angle 0.69205 / 0.36 (27996) SS BOND : bond 0.00401 / 0.26 ( 33) SS BOND : angle 1.19686 / 0.84 ( 66) hydrogen bonds : bond 0.04533 / 2.97 ( 807) hydrogen bonds : angle 5.71498 / 4.05 ( 2142) link_ALPHA1-2 : bond 0.00205 / 0.10 ( 3) link_ALPHA1-2 : angle 2.19913 / 1.07 ( 9) link_ALPHA1-3 : bond 0.00446 / 0.23 ( 3) link_ALPHA1-3 : angle 1.40002 / 0.74 ( 9) link_BETA1-4 : bond 0.00182 / 0.09 ( 9) link_BETA1-4 : angle 2.51680 / 1.40 ( 27) link_NAG-ASN : bond 0.00223 / 0.15 ( 33) link_NAG-ASN : angle 2.03902 / 1.36 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 341 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6281 (p0) cc_final: 0.5791 (p0) REVERT: L 70 GLU cc_start: 0.6808 (mp0) cc_final: 0.6529 (mp0) REVERT: C 80 ASP cc_start: 0.6081 (m-30) cc_final: 0.5689 (t70) REVERT: C 94 GLN cc_start: 0.6765 (tp40) cc_final: 0.5894 (tp-100) REVERT: H 3 GLN cc_start: 0.8313 (pm20) cc_final: 0.8071 (pm20) REVERT: H 19 LYS cc_start: 0.7908 (mmmt) cc_final: 0.6952 (tmtt) REVERT: H 39 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6457 (tp-100) REVERT: H 48 MET cc_start: 0.7635 (ttp) cc_final: 0.7298 (ttt) REVERT: H 91 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.5606 (p90) REVERT: H 97 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7581 (mm-30) REVERT: D 64 GLU cc_start: 0.7756 (tm-30) cc_final: 0.6912 (tt0) REVERT: F 70 GLU cc_start: 0.6862 (mp0) cc_final: 0.6483 (mp0) REVERT: I 46 GLU cc_start: 0.6048 (pt0) cc_final: 0.4986 (tt0) REVERT: I 91 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5269 (p90) REVERT: J 64 GLU cc_start: 0.7674 (tm-30) cc_final: 0.6855 (tt0) REVERT: J 65 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6612 (t) REVERT: J 82 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6760 (mm-40) REVERT: J 435 TYR cc_start: 0.7979 (m-80) cc_final: 0.7599 (m-10) REVERT: K 565 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6177 (ttp) REVERT: K 615 SER cc_start: 0.9128 (t) cc_final: 0.8894 (m) REVERT: M 24 ARG cc_start: 0.6994 (ttm110) cc_final: 0.6738 (ttm-80) REVERT: M 36 TYR cc_start: 0.7427 (m-80) cc_final: 0.6918 (m-80) REVERT: N 58 ARG cc_start: 0.8340 (mtp85) cc_final: 0.8118 (ttt90) REVERT: O 46 GLU cc_start: 0.6652 (pt0) cc_final: 0.5958 (mm-30) outliers start: 87 outliers final: 54 residues processed: 391 average time/residue: 0.1262 time to fit residues: 80.0844 Evaluate side-chains 358 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 522 PHE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 325 ASN A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN F 42 GLN J 80 ASN J 216 HIS J 363 HIS J 417 GLN ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.162080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.135732 restraints weight = 33889.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.138058 restraints weight = 17899.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.139539 restraints weight = 10903.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.140256 restraints weight = 9753.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.140266 restraints weight = 8060.935| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20718 Z= 0.184 Angle : 0.679 10.508 28206 Z= 0.347 Chirality : 0.047 0.178 3261 Planarity : 0.005 0.057 3519 Dihedral : 5.107 31.253 2688 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.00 % Allowed : 14.34 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2427 helix: 0.92 (0.25), residues: 441 sheet: 0.81 (0.24), residues: 546 loop : -0.90 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 54 TYR 0.033 0.002 TYR M 49 PHE 0.024 0.002 PHE B 522 TRP 0.028 0.002 TRP H 36 HIS 0.005 0.001 HIS J 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (20637) covalent geometry : angle 0.66297 / 0.34 (27996) SS BOND : bond 0.00384 / 0.24 ( 33) SS BOND : angle 1.39362 / 0.98 ( 66) hydrogen bonds : bond 0.04318 / 2.83 ( 807) hydrogen bonds : angle 5.59437 / 3.95 ( 2142) link_ALPHA1-2 : bond 0.00273 / 0.14 ( 3) link_ALPHA1-2 : angle 2.20689 / 1.08 ( 9) link_ALPHA1-3 : bond 0.00485 / 0.24 ( 3) link_ALPHA1-3 : angle 1.37042 / 0.73 ( 9) link_BETA1-4 : bond 0.00216 / 0.11 ( 9) link_BETA1-4 : angle 2.33002 / 1.30 ( 27) link_NAG-ASN : bond 0.00181 / 0.12 ( 33) link_NAG-ASN : angle 1.87222 / 1.25 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 331 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.8517 (mp) cc_final: 0.8145 (mt) REVERT: L 70 GLU cc_start: 0.6785 (mp0) cc_final: 0.6509 (mp0) REVERT: C 80 ASP cc_start: 0.6016 (m-30) cc_final: 0.5532 (t0) REVERT: C 94 GLN cc_start: 0.6953 (tp40) cc_final: 0.6136 (tp-100) REVERT: H 3 GLN cc_start: 0.8248 (pm20) cc_final: 0.8027 (pm20) REVERT: H 39 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6318 (tp-100) REVERT: H 91 PHE cc_start: 0.6542 (OUTLIER) cc_final: 0.5634 (p90) REVERT: D 64 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6901 (tt0) REVERT: E 629 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7448 (mmm) REVERT: F 70 GLU cc_start: 0.6884 (mp0) cc_final: 0.6522 (mp0) REVERT: G 58 ARG cc_start: 0.8290 (ttt90) cc_final: 0.8073 (ttt90) REVERT: G 80 ASP cc_start: 0.5814 (m-30) cc_final: 0.5414 (t0) REVERT: I 46 GLU cc_start: 0.6084 (pt0) cc_final: 0.5451 (tt0) REVERT: I 72 ASP cc_start: 0.7705 (t0) cc_final: 0.7145 (t0) REVERT: I 91 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5441 (p90) REVERT: J 64 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6809 (tt0) REVERT: J 65 VAL cc_start: 0.6911 (OUTLIER) cc_final: 0.6706 (t) REVERT: J 435 TYR cc_start: 0.8044 (m-80) cc_final: 0.7631 (m-10) REVERT: K 565 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6121 (ttp) REVERT: K 615 SER cc_start: 0.9112 (t) cc_final: 0.8881 (m) REVERT: K 657 GLU cc_start: 0.7552 (tt0) cc_final: 0.7299 (tt0) REVERT: M 24 ARG cc_start: 0.7060 (ttm110) cc_final: 0.6711 (ttm-80) REVERT: M 36 TYR cc_start: 0.7413 (m-80) cc_final: 0.7145 (m-80) REVERT: N 58 ARG cc_start: 0.8294 (mtp85) cc_final: 0.8062 (ttt90) REVERT: O 23 LYS cc_start: 0.7856 (tppt) cc_final: 0.7562 (tppt) REVERT: O 46 GLU cc_start: 0.6539 (pt0) cc_final: 0.5845 (tt0) REVERT: O 48 MET cc_start: 0.7715 (ttm) cc_final: 0.7215 (ttt) REVERT: O 62 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.8137 (p90) outliers start: 86 outliers final: 57 residues processed: 380 average time/residue: 0.1301 time to fit residues: 80.0976 Evaluate side-chains 361 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 297 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 522 PHE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 220 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 216 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS F 42 GLN J 363 HIS J 417 GLN ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.164750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.138018 restraints weight = 33702.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.140736 restraints weight = 18450.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.143155 restraints weight = 10673.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.143724 restraints weight = 8111.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.144192 restraints weight = 7137.544| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20718 Z= 0.131 Angle : 0.623 7.927 28206 Z= 0.319 Chirality : 0.045 0.184 3261 Planarity : 0.004 0.053 3519 Dihedral : 4.842 17.998 2688 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.31 % Allowed : 15.08 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2427 helix: 1.17 (0.26), residues: 441 sheet: 0.85 (0.24), residues: 549 loop : -0.86 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 54 TYR 0.036 0.002 TYR M 49 PHE 0.016 0.001 PHE K 522 TRP 0.024 0.001 TRP H 36 HIS 0.006 0.001 HIS J 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (20637) covalent geometry : angle 0.61257 / 0.32 (27996) SS BOND : bond 0.00271 / 0.16 ( 33) SS BOND : angle 0.92710 / 0.64 ( 66) hydrogen bonds : bond 0.03881 / 2.56 ( 807) hydrogen bonds : angle 5.40550 / 3.80 ( 2142) link_ALPHA1-2 : bond 0.00142 / 0.07 ( 3) link_ALPHA1-2 : angle 2.06340 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00592 / 0.29 ( 3) link_ALPHA1-3 : angle 1.19887 / 0.64 ( 9) link_BETA1-4 : bond 0.00343 / 0.16 ( 9) link_BETA1-4 : angle 1.95149 / 1.08 ( 27) link_NAG-ASN : bond 0.00157 / 0.09 ( 33) link_NAG-ASN : angle 1.53688 / 1.03 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 354 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8047 (mtm) cc_final: 0.7771 (mtm) REVERT: A 446 SER cc_start: 0.8907 (m) cc_final: 0.8157 (p) REVERT: L 38 GLN cc_start: 0.5043 (OUTLIER) cc_final: 0.4679 (tp40) REVERT: L 70 GLU cc_start: 0.6787 (mp0) cc_final: 0.6554 (mp0) REVERT: C 80 ASP cc_start: 0.5766 (m-30) cc_final: 0.5405 (t70) REVERT: C 94 GLN cc_start: 0.6762 (tp40) cc_final: 0.6209 (tp-100) REVERT: H 3 GLN cc_start: 0.8265 (pm20) cc_final: 0.8058 (pm20) REVERT: H 12 LYS cc_start: 0.6210 (ttmt) cc_final: 0.5815 (ttmt) REVERT: H 39 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6130 (tp-100) REVERT: H 91 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.5647 (p90) REVERT: H 97 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7273 (mp0) REVERT: D 64 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6685 (tt0) REVERT: D 446 SER cc_start: 0.8940 (m) cc_final: 0.8226 (p) REVERT: E 567 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7178 (tp40) REVERT: E 629 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7229 (mmm) REVERT: F 1 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6397 (tm-30) REVERT: F 70 GLU cc_start: 0.6728 (mp0) cc_final: 0.6490 (mp0) REVERT: G 54 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7994 (mtp180) REVERT: G 58 ARG cc_start: 0.8085 (ttt90) cc_final: 0.7850 (ttt90) REVERT: G 80 ASP cc_start: 0.5741 (m-30) cc_final: 0.5311 (t0) REVERT: I 23 LYS cc_start: 0.7394 (tppt) cc_final: 0.6960 (tppt) REVERT: I 46 GLU cc_start: 0.6061 (pt0) cc_final: 0.5730 (tt0) REVERT: I 72 ASP cc_start: 0.7781 (t0) cc_final: 0.7249 (t0) REVERT: I 91 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5535 (p90) REVERT: J 64 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6711 (tt0) REVERT: J 65 VAL cc_start: 0.6847 (OUTLIER) cc_final: 0.6581 (t) REVERT: J 435 TYR cc_start: 0.7999 (m-80) cc_final: 0.7555 (m-10) REVERT: K 565 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6059 (ttp) REVERT: K 657 GLU cc_start: 0.7420 (tt0) cc_final: 0.7160 (tt0) REVERT: M 24 ARG cc_start: 0.6990 (ttm110) cc_final: 0.6648 (ttm-80) REVERT: M 36 TYR cc_start: 0.7189 (m-80) cc_final: 0.6786 (m-80) REVERT: N 58 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7840 (ttt-90) REVERT: O 36 TRP cc_start: 0.7552 (m100) cc_final: 0.7193 (m-10) REVERT: O 46 GLU cc_start: 0.5944 (pt0) cc_final: 0.5713 (tt0) REVERT: O 48 MET cc_start: 0.7741 (ttm) cc_final: 0.7286 (ttt) REVERT: O 62 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.8193 (p90) outliers start: 71 outliers final: 43 residues processed: 385 average time/residue: 0.1307 time to fit residues: 81.1050 Evaluate side-chains 369 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 316 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 167 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 96 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 238 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS J 80 ASN ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS J 417 GLN M 79 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.162112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.135652 restraints weight = 33949.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.138785 restraints weight = 17729.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.140210 restraints weight = 10251.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.140689 restraints weight = 8705.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.140973 restraints weight = 7676.767| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20718 Z= 0.176 Angle : 0.655 7.382 28206 Z= 0.336 Chirality : 0.046 0.165 3261 Planarity : 0.005 0.050 3519 Dihedral : 4.888 18.255 2688 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.63 % Allowed : 15.32 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2427 helix: 1.11 (0.25), residues: 441 sheet: 0.73 (0.22), residues: 609 loop : -0.95 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 54 TYR 0.037 0.002 TYR L 49 PHE 0.015 0.002 PHE K 522 TRP 0.017 0.001 TRP H 36 HIS 0.007 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20637) covalent geometry : angle 0.64359 / 0.33 (27996) SS BOND : bond 0.00333 / 0.22 ( 33) SS BOND : angle 0.97005 / 0.68 ( 66) hydrogen bonds : bond 0.04046 / 2.66 ( 807) hydrogen bonds : angle 5.42861 / 3.82 ( 2142) link_ALPHA1-2 : bond 0.00202 / 0.10 ( 3) link_ALPHA1-2 : angle 2.07728 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00517 / 0.26 ( 3) link_ALPHA1-3 : angle 1.37536 / 0.71 ( 9) link_BETA1-4 : bond 0.00234 / 0.11 ( 9) link_BETA1-4 : angle 2.11277 / 1.16 ( 27) link_NAG-ASN : bond 0.00158 / 0.10 ( 33) link_NAG-ASN : angle 1.60047 / 1.07 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 316 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8014 (mtm) cc_final: 0.7752 (mtm) REVERT: L 70 GLU cc_start: 0.6847 (mp0) cc_final: 0.6569 (mp0) REVERT: C 80 ASP cc_start: 0.5867 (m-30) cc_final: 0.5543 (t70) REVERT: C 94 GLN cc_start: 0.6760 (tp40) cc_final: 0.6427 (tp40) REVERT: H 3 GLN cc_start: 0.8287 (pm20) cc_final: 0.8084 (pm20) REVERT: H 39 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6562 (tp-100) REVERT: H 91 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.5614 (p90) REVERT: H 97 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7400 (mp0) REVERT: D 64 GLU cc_start: 0.7718 (tm-30) cc_final: 0.6764 (tt0) REVERT: D 446 SER cc_start: 0.8970 (m) cc_final: 0.8247 (p) REVERT: E 565 MET cc_start: 0.7005 (ptm) cc_final: 0.6604 (ptm) REVERT: E 567 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7238 (tp40) REVERT: E 629 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7227 (mmm) REVERT: F 1 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: F 70 GLU cc_start: 0.6775 (mp0) cc_final: 0.6518 (mp0) REVERT: G 58 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7949 (ttt90) REVERT: G 80 ASP cc_start: 0.5703 (m-30) cc_final: 0.5324 (t0) REVERT: I 46 GLU cc_start: 0.5982 (pt0) cc_final: 0.5662 (tt0) REVERT: I 72 ASP cc_start: 0.7841 (t0) cc_final: 0.7320 (t0) REVERT: I 91 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5590 (p90) REVERT: J 64 GLU cc_start: 0.7658 (tm-30) cc_final: 0.6754 (tt0) REVERT: J 65 VAL cc_start: 0.6861 (OUTLIER) cc_final: 0.6648 (t) REVERT: J 435 TYR cc_start: 0.7988 (m-80) cc_final: 0.7516 (m-10) REVERT: K 565 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6154 (ttp) REVERT: K 629 MET cc_start: 0.8238 (mmm) cc_final: 0.7473 (mmm) REVERT: K 657 GLU cc_start: 0.7614 (tt0) cc_final: 0.7346 (tt0) REVERT: M 24 ARG cc_start: 0.7000 (ttm110) cc_final: 0.6669 (ttm-80) REVERT: M 36 TYR cc_start: 0.7238 (m-80) cc_final: 0.6889 (m-80) REVERT: N 58 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7917 (ttt-90) REVERT: N 74 LEU cc_start: 0.6494 (mt) cc_final: 0.6293 (mt) REVERT: O 36 TRP cc_start: 0.7590 (m100) cc_final: 0.7205 (m-10) REVERT: O 43 GLN cc_start: 0.8024 (tp40) cc_final: 0.7682 (tp40) REVERT: O 48 MET cc_start: 0.7764 (ttm) cc_final: 0.7297 (ttt) outliers start: 78 outliers final: 61 residues processed: 359 average time/residue: 0.1355 time to fit residues: 78.2715 Evaluate side-chains 368 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 181 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 154 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN J 80 ASN ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS K 658 GLN ** M 90 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 = 0.4563 r_free = 0.4563 target = 0.162938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.134738 restraints weight = 33892.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.138359 restraints weight = 17733.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.140806 restraints weight = 11160.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.142447 restraints weight = 8033.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.143305 restraints weight = 6369.985| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20718 Z= 0.154 Angle : 0.640 7.887 28206 Z= 0.328 Chirality : 0.046 0.179 3261 Planarity : 0.004 0.052 3519 Dihedral : 4.844 18.168 2688 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.49 % Allowed : 15.69 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2427 helix: 1.15 (0.25), residues: 441 sheet: 0.73 (0.22), residues: 609 loop : -0.98 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.037 0.002 TYR L 49 PHE 0.014 0.002 PHE A 53 TRP 0.023 0.001 TRP H 36 HIS 0.005 0.001 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (20637) covalent geometry : angle 0.62921 / 0.33 (27996) SS BOND : bond 0.00292 / 0.18 ( 33) SS BOND : angle 0.92089 / 0.65 ( 66) hydrogen bonds : bond 0.03953 / 2.59 ( 807) hydrogen bonds : angle 5.37534 / 3.77 ( 2142) link_ALPHA1-2 : bond 0.00083 / 0.04 ( 3) link_ALPHA1-2 : angle 2.07513 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00530 / 0.26 ( 3) link_ALPHA1-3 : angle 1.34219 / 0.70 ( 9) link_BETA1-4 : bond 0.00236 / 0.12 ( 9) link_BETA1-4 : angle 2.03181 / 1.12 ( 27) link_NAG-ASN : bond 0.00130 / 0.08 ( 33) link_NAG-ASN : angle 1.53704 / 1.04 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 318 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6154 (p0) cc_final: 0.5735 (p0) REVERT: L 70 GLU cc_start: 0.6819 (mp0) cc_final: 0.6529 (mp0) REVERT: C 80 ASP cc_start: 0.5507 (m-30) cc_final: 0.5174 (t70) REVERT: C 94 GLN cc_start: 0.6575 (tp40) cc_final: 0.6273 (tp-100) REVERT: H 3 GLN cc_start: 0.8291 (pm20) cc_final: 0.8082 (pm20) REVERT: H 39 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6523 (tp-100) REVERT: H 91 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.5646 (p90) REVERT: H 97 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7310 (mm-30) REVERT: D 64 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6682 (tt0) REVERT: D 80 ASN cc_start: 0.6105 (p0) cc_final: 0.5887 (p0) REVERT: D 446 SER cc_start: 0.8945 (m) cc_final: 0.8214 (p) REVERT: E 565 MET cc_start: 0.6864 (ptm) cc_final: 0.6576 (ttp) REVERT: E 567 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7213 (tp40) REVERT: E 629 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7163 (mmm) REVERT: F 70 GLU cc_start: 0.6743 (mp0) cc_final: 0.6524 (mp0) REVERT: G 58 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7929 (ttt90) REVERT: G 80 ASP cc_start: 0.5659 (m-30) cc_final: 0.5304 (t0) REVERT: I 12 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7116 (ttmt) REVERT: I 46 GLU cc_start: 0.6007 (pt0) cc_final: 0.5786 (tt0) REVERT: I 91 PHE cc_start: 0.6313 (OUTLIER) cc_final: 0.5641 (p90) REVERT: J 64 GLU cc_start: 0.7598 (tm-30) cc_final: 0.6703 (tt0) REVERT: J 65 VAL cc_start: 0.6940 (OUTLIER) cc_final: 0.6715 (t) REVERT: J 82 GLN cc_start: 0.7534 (tp40) cc_final: 0.7135 (tp40) REVERT: J 435 TYR cc_start: 0.7988 (m-80) cc_final: 0.7525 (m-10) REVERT: K 565 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.5729 (ttm) REVERT: K 657 GLU cc_start: 0.7554 (tt0) cc_final: 0.7243 (tt0) REVERT: M 24 ARG cc_start: 0.7008 (ttm110) cc_final: 0.6676 (ttm-80) REVERT: M 36 TYR cc_start: 0.7158 (m-80) cc_final: 0.6870 (m-80) REVERT: N 58 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7878 (ttt-90) REVERT: N 74 LEU cc_start: 0.6661 (mt) cc_final: 0.6415 (mt) REVERT: O 43 GLN cc_start: 0.8029 (tp40) cc_final: 0.7706 (tp40) REVERT: O 48 MET cc_start: 0.7734 (ttm) cc_final: 0.7296 (ttt) REVERT: O 62 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.8097 (p90) REVERT: O 72 ASP cc_start: 0.7826 (t0) cc_final: 0.7255 (t0) outliers start: 75 outliers final: 58 residues processed: 364 average time/residue: 0.1365 time to fit residues: 80.4199 Evaluate side-chains 363 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 91 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 76 optimal weight: 0.0020 chunk 19 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 229 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 229 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN J 80 ASN J 363 HIS ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.160969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.134521 restraints weight = 33734.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.138191 restraints weight = 17721.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.139100 restraints weight = 10345.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.139857 restraints weight = 8825.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.139749 restraints weight = 7616.777| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20718 Z= 0.191 Angle : 0.672 8.644 28206 Z= 0.344 Chirality : 0.047 0.164 3261 Planarity : 0.005 0.048 3519 Dihedral : 4.944 18.178 2688 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.86 % Allowed : 15.18 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2427 helix: 1.08 (0.25), residues: 441 sheet: 0.65 (0.22), residues: 612 loop : -1.09 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 54 TYR 0.038 0.002 TYR M 49 PHE 0.014 0.002 PHE B 522 TRP 0.021 0.002 TRP O 36 HIS 0.006 0.001 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (20637) covalent geometry : angle 0.66102 / 0.34 (27996) SS BOND : bond 0.00354 / 0.23 ( 33) SS BOND : angle 1.00878 / 0.71 ( 66) hydrogen bonds : bond 0.04135 / 2.71 ( 807) hydrogen bonds : angle 5.43762 / 3.82 ( 2142) link_ALPHA1-2 : bond 0.00173 / 0.09 ( 3) link_ALPHA1-2 : angle 2.13961 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00475 / 0.24 ( 3) link_ALPHA1-3 : angle 1.40117 / 0.75 ( 9) link_BETA1-4 : bond 0.00148 / 0.07 ( 9) link_BETA1-4 : angle 2.15429 / 1.18 ( 27) link_NAG-ASN : bond 0.00171 / 0.11 ( 33) link_NAG-ASN : angle 1.63873 / 1.11 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 GLN cc_start: 0.6891 (tp40) cc_final: 0.6684 (tp40) REVERT: H 3 GLN cc_start: 0.8333 (pm20) cc_final: 0.8130 (pm20) REVERT: H 39 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6507 (tp-100) REVERT: H 72 ASP cc_start: 0.7596 (t0) cc_final: 0.7290 (t0) REVERT: H 91 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5782 (p90) REVERT: H 97 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7216 (mm-30) REVERT: D 64 GLU cc_start: 0.7753 (tm-30) cc_final: 0.6759 (tt0) REVERT: E 565 MET cc_start: 0.6958 (ptm) cc_final: 0.6738 (ttp) REVERT: E 567 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7274 (tp40) REVERT: E 629 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7197 (mmm) REVERT: F 70 GLU cc_start: 0.6784 (mp0) cc_final: 0.6560 (mp0) REVERT: G 54 ARG cc_start: 0.8419 (mtp-110) cc_final: 0.8132 (mtp180) REVERT: G 58 ARG cc_start: 0.8246 (ttt90) cc_final: 0.8019 (ttt90) REVERT: G 80 ASP cc_start: 0.5839 (m-30) cc_final: 0.5436 (t0) REVERT: I 3 GLN cc_start: 0.8181 (mp10) cc_final: 0.7950 (mp10) REVERT: I 12 LYS cc_start: 0.7358 (ttmt) cc_final: 0.7087 (ttmt) REVERT: I 46 GLU cc_start: 0.6052 (pt0) cc_final: 0.5727 (tt0) REVERT: I 91 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5706 (p90) REVERT: J 82 GLN cc_start: 0.7672 (tp40) cc_final: 0.7286 (tp40) REVERT: J 435 TYR cc_start: 0.8029 (m-80) cc_final: 0.7570 (m-10) REVERT: K 657 GLU cc_start: 0.7691 (tt0) cc_final: 0.7401 (tt0) REVERT: M 24 ARG cc_start: 0.7070 (ttm110) cc_final: 0.6802 (ttm-80) REVERT: M 36 TYR cc_start: 0.7242 (m-80) cc_final: 0.7009 (m-80) REVERT: M 37 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6621 (pp30) REVERT: N 58 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7900 (ttt-90) REVERT: O 12 LYS cc_start: 0.6147 (ttmt) cc_final: 0.5749 (tttt) REVERT: O 48 MET cc_start: 0.7763 (ttm) cc_final: 0.7492 (ttt) REVERT: O 62 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.8082 (p90) REVERT: O 72 ASP cc_start: 0.7950 (t0) cc_final: 0.7333 (t0) outliers start: 83 outliers final: 66 residues processed: 375 average time/residue: 0.1351 time to fit residues: 82.3243 Evaluate side-chains 378 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 305 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain E residue 644 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 619 ILE Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Chi-restraints excluded: chain O residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 363 HIS ** M 90 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 = 0.4570 r_free = 0.4570 target = 0.163393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.135666 restraints weight = 33858.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.139341 restraints weight = 17650.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.141829 restraints weight = 11023.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.143391 restraints weight = 7914.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.144326 restraints weight = 6312.328| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20718 Z= 0.142 Angle : 0.651 9.945 28206 Z= 0.335 Chirality : 0.046 0.173 3261 Planarity : 0.005 0.082 3519 Dihedral : 4.841 18.020 2688 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.35 % Allowed : 16.20 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2427 helix: 1.27 (0.26), residues: 441 sheet: 0.80 (0.23), residues: 579 loop : -1.05 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 54 TYR 0.039 0.002 TYR M 49 PHE 0.014 0.001 PHE A 53 TRP 0.044 0.002 TRP O 36 HIS 0.006 0.001 HIS J 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (20637) covalent geometry : angle 0.64171 / 0.33 (27996) SS BOND : bond 0.00279 / 0.17 ( 33) SS BOND : angle 0.88068 / 0.62 ( 66) hydrogen bonds : bond 0.03852 / 2.53 ( 807) hydrogen bonds : angle 5.34006 / 3.74 ( 2142) link_ALPHA1-2 : bond 0.00209 / 0.11 ( 3) link_ALPHA1-2 : angle 2.08319 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00679 / 0.34 ( 3) link_ALPHA1-3 : angle 1.28142 / 0.68 ( 9) link_BETA1-4 : bond 0.00264 / 0.12 ( 9) link_BETA1-4 : angle 1.90733 / 1.05 ( 27) link_NAG-ASN : bond 0.00116 / 0.07 ( 33) link_NAG-ASN : angle 1.48640 / 1.01 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 325 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 SER cc_start: 0.8950 (m) cc_final: 0.8187 (p) REVERT: L 37 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: L 70 GLU cc_start: 0.6862 (mp0) cc_final: 0.6612 (mp0) REVERT: C 94 GLN cc_start: 0.6448 (tp40) cc_final: 0.6203 (tp40) REVERT: H 39 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6528 (tp-100) REVERT: H 91 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5694 (p90) REVERT: D 64 GLU cc_start: 0.7644 (tm-30) cc_final: 0.6769 (tt0) REVERT: D 446 SER cc_start: 0.8934 (m) cc_final: 0.8192 (p) REVERT: E 565 MET cc_start: 0.6940 (ptm) cc_final: 0.6714 (ttp) REVERT: E 567 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7250 (tp40) REVERT: E 629 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6653 (mmm) REVERT: G 80 ASP cc_start: 0.5791 (m-30) cc_final: 0.5412 (t0) REVERT: I 3 GLN cc_start: 0.8140 (mp10) cc_final: 0.7886 (mp10) REVERT: I 12 LYS cc_start: 0.7409 (ttmt) cc_final: 0.6974 (ttmt) REVERT: I 91 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5446 (p90) REVERT: J 435 TYR cc_start: 0.7971 (m-80) cc_final: 0.7500 (m-10) REVERT: K 565 MET cc_start: 0.6540 (ptm) cc_final: 0.5839 (ttm) REVERT: K 657 GLU cc_start: 0.7522 (tt0) cc_final: 0.7230 (tt0) REVERT: M 36 TYR cc_start: 0.7174 (m-80) cc_final: 0.6942 (m-80) REVERT: M 37 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6613 (pp30) REVERT: M 70 GLU cc_start: 0.5842 (mm-30) cc_final: 0.5529 (mp0) REVERT: N 58 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7824 (ttt-90) REVERT: O 62 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7996 (p90) REVERT: O 72 ASP cc_start: 0.8070 (t0) cc_final: 0.7513 (t0) outliers start: 72 outliers final: 56 residues processed: 368 average time/residue: 0.1321 time to fit residues: 79.6698 Evaluate side-chains 367 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain E residue 567 GLN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 638 TYR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 378 CYS Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain K residue 540 GLN Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 62 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 175 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 363 HIS ** M 90 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 = 0.4568 r_free = 0.4568 target = 0.163297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.135615 restraints weight = 34233.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.139216 restraints weight = 17901.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.141630 restraints weight = 11291.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.143220 restraints weight = 8155.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.144132 restraints weight = 6499.610| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 20718 Z= 0.206 Angle : 0.814 59.195 28206 Z= 0.461 Chirality : 0.047 0.296 3261 Planarity : 0.006 0.132 3519 Dihedral : 4.884 27.765 2688 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.26 % Allowed : 16.57 % Favored : 80.17 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2427 helix: 1.20 (0.26), residues: 441 sheet: 0.78 (0.23), residues: 579 loop : -1.08 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 54 TYR 0.037 0.002 TYR M 49 PHE 0.014 0.002 PHE A 53 TRP 0.048 0.002 TRP O 36 HIS 0.006 0.001 HIS J 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (20637) covalent geometry : angle 0.80764 / 0.46 (27996) SS BOND : bond 0.00309 / 0.19 ( 33) SS BOND : angle 0.88122 / 0.61 ( 66) hydrogen bonds : bond 0.03891 / 2.55 ( 807) hydrogen bonds : angle 5.34507 / 3.75 ( 2142) link_ALPHA1-2 : bond 0.00238 / 0.13 ( 3) link_ALPHA1-2 : angle 2.16488 / 1.04 ( 9) link_ALPHA1-3 : bond 0.00373 / 0.19 ( 3) link_ALPHA1-3 : angle 1.25471 / 0.67 ( 9) link_BETA1-4 : bond 0.00245 / 0.11 ( 9) link_BETA1-4 : angle 1.95048 / 1.07 ( 27) link_NAG-ASN : bond 0.00124 / 0.07 ( 33) link_NAG-ASN : angle 1.49669 / 1.02 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.36 seconds wall clock time: 63 minutes 5.27 seconds (3785.27 seconds total)