Starting phenix.real_space_refine on Thu Mar 5 07:23:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x5b_22048/03_2026/6x5b_22048.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x5b_22048/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6x5b_22048/03_2026/6x5b_22048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x5b_22048/03_2026/6x5b_22048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x5b_22048/03_2026/6x5b_22048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x5b_22048/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 24 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 dihedrals: 3 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: 3.39, per 1000 atoms: 0.17 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: 1.57 Conformation dependent library (CDL) restraints added in 821.8 milliseconds 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: 0.90 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: 4.10 Time building geometry restraints manager: 2.15 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 - 21.73: 12639 21.73 - 43.47: 255 43.47 - 65.20: 96 65.20 - 86.93: 27 86.93 - 108.66: 12 Dihedral angle restraints: 13029 sinusoidal: 5886 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 13026 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: 0.05 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.080 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 11.149 108.664 8316 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 covalent geometry : bond 0.02125 (20637) covalent geometry : angle 1.74615 (27996) SS BOND : bond 0.02011 ( 33) SS BOND : angle 2.73696 ( 66) hydrogen bonds : bond 0.15974 ( 807) hydrogen bonds : angle 7.78402 ( 2142) link_ALPHA1-2 : bond 0.07306 ( 3) link_ALPHA1-2 : angle 4.48488 ( 9) link_ALPHA1-3 : bond 0.05282 ( 3) link_ALPHA1-3 : angle 2.31705 ( 9) link_BETA1-4 : bond 0.06762 ( 9) link_BETA1-4 : angle 5.11325 ( 27) link_NAG-ASN : bond 0.08252 ( 33) link_NAG-ASN : angle 2.67976 ( 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 : 0.566 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: 0.1463 time to fit residues: 154.2300 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 : 0.672 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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 M 93 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 = 0.4642 r_free = 0.4642 target = 0.169451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.143106 restraints weight = 33193.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.145852 restraints weight = 17647.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.147132 restraints weight = 10127.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.147778 restraints weight = 8918.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.148044 restraints weight = 7816.431| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3420 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= 0.213 Angle : 0.800 11.838 28206 Z= 0.412 Chirality : 0.050 0.201 3261 Planarity : 0.005 0.050 3519 Dihedral : 7.756 69.045 3678 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.75 % Allowed : 9.36 % Favored : 87.90 % 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: 0.42 (0.17), residues: 2427 helix: 0.66 (0.24), residues: 456 sheet: 0.87 (0.22), residues: 591 loop : -0.04 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 50 TYR 0.030 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 covalent geometry : bond 0.00479 (20637) covalent geometry : angle 0.77788 (27996) SS BOND : bond 0.00474 ( 33) SS BOND : angle 1.18732 ( 66) hydrogen bonds : bond 0.05194 ( 807) hydrogen bonds : angle 5.89958 ( 2142) link_ALPHA1-2 : bond 0.00121 ( 3) link_ALPHA1-2 : angle 2.46883 ( 9) link_ALPHA1-3 : bond 0.01020 ( 3) link_ALPHA1-3 : angle 2.64659 ( 9) link_BETA1-4 : bond 0.00325 ( 9) link_BETA1-4 : angle 3.27800 ( 27) link_NAG-ASN : bond 0.00542 ( 33) link_NAG-ASN : angle 2.51470 ( 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 472 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 413 time to evaluate : 0.740 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: A 64 GLU cc_start: 0.7590 (tm-30) cc_final: 0.6743 (tt0) REVERT: A 345 ILE cc_start: 0.7964 (mt) cc_final: 0.7722 (mp) REVERT: A 426 MET cc_start: 0.7649 (mtp) cc_final: 0.7379 (mtp) REVERT: A 428 GLN cc_start: 0.8288 (mp10) cc_final: 0.7821 (mt0) REVERT: A 434 MET cc_start: 0.7368 (ttp) cc_final: 0.7166 (tmm) REVERT: A 446 SER cc_start: 0.8781 (m) cc_final: 0.8054 (p) REVERT: B 657 GLU cc_start: 0.7606 (tt0) cc_final: 0.7213 (tt0) REVERT: L 2 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4745 (mt) REVERT: C 86 VAL cc_start: 0.8320 (t) cc_final: 0.8098 (p) REVERT: C 94 GLN cc_start: 0.6596 (tp40) cc_final: 0.5786 (tp40) REVERT: H 3 GLN cc_start: 0.8304 (pm20) cc_final: 0.8036 (pm20) REVERT: H 19 LYS cc_start: 0.7164 (tptm) cc_final: 0.6886 (mmmt) REVERT: D 64 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6755 (tt0) REVERT: D 446 SER cc_start: 0.8706 (m) cc_final: 0.7921 (p) REVERT: E 565 MET cc_start: 0.6724 (ptm) cc_final: 0.6153 (ptm) REVERT: E 632 GLU cc_start: 0.7904 (tp30) cc_final: 0.7673 (tm-30) REVERT: E 638 TYR cc_start: 0.6781 (m-80) cc_final: 0.6556 (m-10) REVERT: F 2 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4349 (mt) REVERT: F 70 GLU cc_start: 0.6765 (mp0) cc_final: 0.6442 (mp0) REVERT: G 58 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7388 (ttt90) REVERT: G 86 VAL cc_start: 0.8236 (t) cc_final: 0.7739 (p) REVERT: I 12 LYS cc_start: 0.7504 (mmtt) cc_final: 0.6800 (mmtt) REVERT: I 52 ILE cc_start: 0.7664 (mm) cc_final: 0.7432 (mp) REVERT: J 64 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6645 (tt0) REVERT: J 435 TYR cc_start: 0.7977 (m-80) cc_final: 0.7698 (m-10) REVERT: J 446 SER cc_start: 0.8826 (m) cc_final: 0.8324 (p) REVERT: M 2 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4166 (mt) REVERT: M 24 ARG cc_start: 0.6956 (ttm110) cc_final: 0.6656 (ttm-80) REVERT: N 58 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7778 (ttt-90) REVERT: N 71 ILE cc_start: 0.7530 (mt) cc_final: 0.7204 (tt) REVERT: N 74 LEU cc_start: 0.6019 (tt) cc_final: 0.5561 (tp) REVERT: O 12 LYS cc_start: 0.6769 (mptt) cc_final: 0.5372 (mttp) outliers start: 59 outliers final: 27 residues processed: 450 average time/residue: 0.1355 time to fit residues: 93.9981 Evaluate side-chains 354 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 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 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 646 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 199 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN H 82BASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN E 653 GLN F 42 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS K 620 ASN ** 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 = 0.4655 r_free = 0.4655 target = 0.170375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.144266 restraints weight = 33325.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.147012 restraints weight = 17909.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.148260 restraints weight = 10281.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.149346 restraints weight = 9074.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.149547 restraints weight = 7406.481| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20718 Z= 0.141 Angle : 0.670 9.720 28206 Z= 0.342 Chirality : 0.046 0.166 3261 Planarity : 0.005 0.059 3519 Dihedral : 6.453 50.876 3678 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.51 % Allowed : 12.43 % Favored : 85.06 % 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: 0.26 (0.17), residues: 2427 helix: 0.83 (0.25), residues: 459 sheet: 0.79 (0.22), residues: 570 loop : -0.27 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 54 TYR 0.026 0.002 TYR H 100E PHE 0.015 0.002 PHE D 53 TRP 0.039 0.001 TRP H 36 HIS 0.008 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00312 (20637) covalent geometry : angle 0.65425 (27996) SS BOND : bond 0.00312 ( 33) SS BOND : angle 1.17705 ( 66) hydrogen bonds : bond 0.04376 ( 807) hydrogen bonds : angle 5.58902 ( 2142) link_ALPHA1-2 : bond 0.00194 ( 3) link_ALPHA1-2 : angle 2.36891 ( 9) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 1.57803 ( 9) link_BETA1-4 : bond 0.00662 ( 9) link_BETA1-4 : angle 2.51628 ( 27) link_NAG-ASN : bond 0.00282 ( 33) link_NAG-ASN : angle 1.89530 ( 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 430 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 376 time to evaluate : 0.767 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: 0.7663 (tm-30) cc_final: 0.6792 (tt0) REVERT: A 328 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: A 434 MET cc_start: 0.7266 (ttp) cc_final: 0.7062 (tmm) REVERT: A 446 SER cc_start: 0.8746 (m) cc_final: 0.8030 (p) REVERT: A 475 MET cc_start: 0.7507 (mmt) cc_final: 0.7252 (mmm) REVERT: C 94 GLN cc_start: 0.6685 (tp40) cc_final: 0.6239 (tp40) REVERT: H 3 GLN cc_start: 0.8259 (pm20) cc_final: 0.7996 (pm20) REVERT: H 10 GLU cc_start: 0.5076 (tm-30) cc_final: 0.4689 (tm-30) REVERT: D 64 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6645 (tt0) REVERT: E 565 MET cc_start: 0.6828 (ptm) cc_final: 0.6276 (ptm) REVERT: G 58 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7366 (ttt90) REVERT: I 19 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6635 (tmtt) REVERT: I 23 LYS cc_start: 0.7235 (tppt) cc_final: 0.6880 (tppt) REVERT: I 31 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7663 (mtt-85) REVERT: J 64 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6433 (tt0) REVERT: J 435 TYR cc_start: 0.7982 (m-80) cc_final: 0.7583 (m-10) REVERT: J 446 SER cc_start: 0.8783 (m) cc_final: 0.8280 (p) REVERT: M 24 ARG cc_start: 0.7023 (ttm110) cc_final: 0.6724 (ttm-80) REVERT: N 58 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7739 (ttt-90) REVERT: O 46 GLU cc_start: 0.6504 (pt0) cc_final: 0.5710 (tt0) REVERT: O 99 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7875 (mm-30) REVERT: O 108 LEU cc_start: 0.8125 (pp) cc_final: 0.7895 (tt) outliers start: 54 outliers final: 29 residues processed: 404 average time/residue: 0.1316 time to fit residues: 83.6589 Evaluate side-chains 347 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 316 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 328 GLN 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 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 70 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 485 LYS 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 34 ILE 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 70 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 108 LEU 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 O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 237 optimal weight: 4.9990 chunk 226 optimal weight: 0.4980 chunk 173 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 57 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 80 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** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 93 ASN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN M 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.165706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.139493 restraints weight = 33521.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.142841 restraints weight = 17499.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.144025 restraints weight = 10230.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.145330 restraints weight = 8869.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.145487 restraints weight = 7569.048| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 20718 Z= 0.185 Angle : 0.691 9.807 28206 Z= 0.352 Chirality : 0.047 0.201 3261 Planarity : 0.005 0.056 3519 Dihedral : 5.646 29.949 3678 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.49 % Allowed : 12.85 % Favored : 83.66 % 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: 0.01 (0.17), residues: 2427 helix: 0.98 (0.25), residues: 441 sheet: 0.80 (0.23), residues: 549 loop : -0.62 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 54 TYR 0.032 0.002 TYR M 49 PHE 0.030 0.002 PHE J 53 TRP 0.021 0.002 TRP H 36 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00430 (20637) covalent geometry : angle 0.67017 (27996) SS BOND : bond 0.00992 ( 33) SS BOND : angle 2.03363 ( 66) hydrogen bonds : bond 0.04394 ( 807) hydrogen bonds : angle 5.43693 ( 2142) link_ALPHA1-2 : bond 0.00191 ( 3) link_ALPHA1-2 : angle 2.39541 ( 9) link_ALPHA1-3 : bond 0.00951 ( 3) link_ALPHA1-3 : angle 1.99733 ( 9) link_BETA1-4 : bond 0.00329 ( 9) link_BETA1-4 : angle 2.52360 ( 27) link_NAG-ASN : bond 0.00220 ( 33) link_NAG-ASN : angle 1.90347 ( 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 430 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 355 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7745 (tm-30) cc_final: 0.6884 (tt0) REVERT: A 446 SER cc_start: 0.8853 (m) cc_final: 0.8089 (p) REVERT: A 475 MET cc_start: 0.7513 (mmt) cc_final: 0.7281 (mmm) REVERT: B 632 GLU cc_start: 0.7941 (tp30) cc_final: 0.7644 (tm-30) REVERT: H 19 LYS cc_start: 0.6833 (tptp) cc_final: 0.5555 (tptp) REVERT: H 39 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6361 (tp-100) REVERT: D 64 GLU cc_start: 0.7740 (tm-30) cc_final: 0.6856 (tt0) REVERT: E 632 GLU cc_start: 0.8138 (tp30) cc_final: 0.7868 (tm-30) REVERT: E 638 TYR cc_start: 0.6880 (m-80) cc_final: 0.6551 (m-80) REVERT: G 31 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8538 (p) REVERT: G 54 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8026 (mtp180) REVERT: I 46 GLU cc_start: 0.6454 (pt0) cc_final: 0.5371 (tt0) REVERT: I 91 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.5502 (p90) REVERT: J 64 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6671 (tt0) REVERT: J 82 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6856 (mm-40) REVERT: J 203 GLN cc_start: 0.7687 (mt0) cc_final: 0.7185 (mt0) REVERT: J 435 TYR cc_start: 0.7943 (m-80) cc_final: 0.7559 (m-10) REVERT: K 565 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6338 (ttp) REVERT: K 657 GLU cc_start: 0.7551 (tt0) cc_final: 0.7241 (tt0) REVERT: M 24 ARG cc_start: 0.6911 (ttm110) cc_final: 0.6646 (ttm-80) REVERT: N 58 ARG cc_start: 0.8251 (mtp85) cc_final: 0.8047 (ttt90) REVERT: N 71 ILE cc_start: 0.7808 (mt) cc_final: 0.7546 (tt) outliers start: 75 outliers final: 49 residues processed: 393 average time/residue: 0.1270 time to fit residues: 80.1679 Evaluate side-chains 368 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 315 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 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 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 LEU 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 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 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 80 ASN 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 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 O residue 10 GLU 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 Chi-restraints excluded: chain O residue 70 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: 2.9990 chunk 25 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 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** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS F 42 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** K 564 HIS ** 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 = 0.4577 r_free = 0.4577 target = 0.164202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.137472 restraints weight = 33685.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.139892 restraints weight = 18692.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.142127 restraints weight = 11043.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.142429 restraints weight = 8279.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.142635 restraints weight = 7904.783| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20718 Z= 0.184 Angle : 0.687 12.549 28206 Z= 0.349 Chirality : 0.047 0.171 3261 Planarity : 0.005 0.053 3519 Dihedral : 5.449 32.643 3678 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.54 % Allowed : 14.06 % Favored : 82.40 % 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: -0.13 (0.17), residues: 2427 helix: 1.00 (0.25), residues: 441 sheet: 0.81 (0.23), residues: 549 loop : -0.80 (0.16), residues: 1437 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 0.015 0.002 PHE D 53 TRP 0.020 0.002 TRP J 45 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00429 (20637) covalent geometry : angle 0.66738 (27996) SS BOND : bond 0.00560 ( 33) SS BOND : angle 1.93086 ( 66) hydrogen bonds : bond 0.04231 ( 807) hydrogen bonds : angle 5.41559 ( 2142) link_ALPHA1-2 : bond 0.00137 ( 3) link_ALPHA1-2 : angle 2.52496 ( 9) link_ALPHA1-3 : bond 0.00895 ( 3) link_ALPHA1-3 : angle 2.00941 ( 9) link_BETA1-4 : bond 0.00284 ( 9) link_BETA1-4 : angle 2.39194 ( 27) link_NAG-ASN : bond 0.00171 ( 33) link_NAG-ASN : angle 1.87919 ( 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 423 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 347 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7797 (tm-30) cc_final: 0.6822 (tt0) REVERT: A 80 ASN cc_start: 0.6225 (p0) cc_final: 0.5601 (p0) REVERT: A 96 TRP cc_start: 0.8539 (m100) cc_final: 0.8288 (m100) REVERT: A 475 MET cc_start: 0.7544 (mmt) cc_final: 0.7324 (mmm) REVERT: B 632 GLU cc_start: 0.7970 (tp30) cc_final: 0.7684 (tm-30) REVERT: C 94 GLN cc_start: 0.5941 (tp40) cc_final: 0.5616 (tp40) REVERT: H 3 GLN cc_start: 0.8288 (pm20) cc_final: 0.8055 (pm20) REVERT: H 39 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6555 (tp-100) REVERT: H 91 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5527 (p90) REVERT: D 64 GLU cc_start: 0.7776 (tm-30) cc_final: 0.6848 (tt0) REVERT: E 567 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7214 (tp40) REVERT: E 629 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7531 (mmm) REVERT: E 638 TYR cc_start: 0.6969 (m-80) cc_final: 0.6729 (m-80) REVERT: G 31 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8494 (p) REVERT: I 46 GLU cc_start: 0.6641 (pt0) cc_final: 0.5588 (tt0) REVERT: I 72 ASP cc_start: 0.7746 (t0) cc_final: 0.7257 (t0) REVERT: I 91 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.5516 (p90) REVERT: J 64 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6761 (tt0) REVERT: J 82 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6753 (mm-40) REVERT: J 203 GLN cc_start: 0.7718 (mt0) cc_final: 0.7404 (mt0) REVERT: J 435 TYR cc_start: 0.8036 (m-80) cc_final: 0.7622 (m-10) REVERT: K 565 MET cc_start: 0.6670 (ptm) cc_final: 0.6212 (ttp) REVERT: K 657 GLU cc_start: 0.7525 (tt0) cc_final: 0.7211 (tt0) REVERT: M 24 ARG cc_start: 0.6990 (ttm110) cc_final: 0.6755 (ttm-80) REVERT: M 36 TYR cc_start: 0.7146 (m-80) cc_final: 0.6586 (m-80) REVERT: N 58 ARG cc_start: 0.8255 (mtp85) cc_final: 0.8025 (ttt90) REVERT: O 12 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6529 (ttmt) REVERT: O 23 LYS cc_start: 0.7860 (tppt) cc_final: 0.7582 (tppt) REVERT: O 46 GLU cc_start: 0.6037 (pt0) cc_final: 0.5500 (tt0) REVERT: O 48 MET cc_start: 0.7645 (ttm) cc_final: 0.7236 (ttt) REVERT: O 97 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7150 (mm-30) outliers start: 76 outliers final: 48 residues processed: 386 average time/residue: 0.1193 time to fit residues: 74.7492 Evaluate side-chains 365 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 61 LEU 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 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 108 LEU 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 426 MET 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 E residue 645 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 3 GLN 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 201 ILE Chi-restraints excluded: chain J residue 373 THR 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 61 LEU Chi-restraints excluded: chain O residue 12 LYS 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 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 204 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN F 79 GLN J 80 ASN M 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.165319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.139302 restraints weight = 33601.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.141794 restraints weight = 17456.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.143981 restraints weight = 10432.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.144228 restraints weight = 8003.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.144428 restraints weight = 7597.108| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20718 Z= 0.147 Angle : 0.643 12.053 28206 Z= 0.329 Chirality : 0.046 0.164 3261 Planarity : 0.005 0.051 3519 Dihedral : 5.246 32.916 3678 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.63 % Allowed : 14.29 % Favored : 82.08 % 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: -0.09 (0.17), residues: 2427 helix: 1.12 (0.26), residues: 441 sheet: 0.80 (0.23), residues: 579 loop : -0.85 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 54 TYR 0.034 0.002 TYR M 49 PHE 0.014 0.001 PHE J 53 TRP 0.029 0.001 TRP H 36 HIS 0.013 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00339 (20637) covalent geometry : angle 0.62852 (27996) SS BOND : bond 0.00359 ( 33) SS BOND : angle 1.41190 ( 66) hydrogen bonds : bond 0.03985 ( 807) hydrogen bonds : angle 5.30323 ( 2142) link_ALPHA1-2 : bond 0.00024 ( 3) link_ALPHA1-2 : angle 2.44719 ( 9) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 1.79997 ( 9) link_BETA1-4 : bond 0.00336 ( 9) link_BETA1-4 : angle 2.12609 ( 27) link_NAG-ASN : bond 0.00134 ( 33) link_NAG-ASN : angle 1.66887 ( 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: 78 poor density : 347 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7737 (tm-30) cc_final: 0.6705 (tt0) REVERT: A 100 MET cc_start: 0.7997 (mtm) cc_final: 0.7705 (mtm) REVERT: A 446 SER cc_start: 0.8869 (m) cc_final: 0.8119 (p) REVERT: A 475 MET cc_start: 0.7557 (mmt) cc_final: 0.7350 (mmm) REVERT: B 632 GLU cc_start: 0.7947 (tp30) cc_final: 0.7653 (tm-30) REVERT: L 38 GLN cc_start: 0.5295 (OUTLIER) cc_final: 0.4907 (tp40) REVERT: C 94 GLN cc_start: 0.6285 (tp40) cc_final: 0.5855 (tp40) REVERT: H 3 GLN cc_start: 0.8294 (pm20) cc_final: 0.8069 (pm20) REVERT: H 39 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6491 (tp-100) REVERT: H 91 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5601 (p90) REVERT: D 64 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6638 (tt0) REVERT: E 567 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7054 (tp40) REVERT: E 629 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7344 (mmm) REVERT: F 2 LEU cc_start: 0.3976 (OUTLIER) cc_final: 0.3398 (mm) REVERT: G 58 ARG cc_start: 0.8108 (ttt90) cc_final: 0.7828 (ttt90) REVERT: G 80 ASP cc_start: 0.5759 (m-30) cc_final: 0.5189 (t0) REVERT: G 94 GLN cc_start: 0.5999 (tp40) cc_final: 0.5612 (tp40) REVERT: I 10 GLU cc_start: 0.3574 (tm-30) cc_final: 0.3176 (tm-30) REVERT: I 23 LYS cc_start: 0.7378 (tppt) cc_final: 0.6935 (tppt) REVERT: I 46 GLU cc_start: 0.6364 (pt0) cc_final: 0.5560 (tt0) REVERT: I 72 ASP cc_start: 0.7732 (t0) cc_final: 0.7240 (t0) REVERT: I 91 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5431 (p90) REVERT: J 64 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6684 (tt0) REVERT: J 435 TYR cc_start: 0.7997 (m-80) cc_final: 0.7608 (m-10) REVERT: K 565 MET cc_start: 0.6576 (ptm) cc_final: 0.6072 (ttp) REVERT: K 657 GLU cc_start: 0.7512 (tt0) cc_final: 0.7212 (tt0) REVERT: M 24 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6715 (ttm-80) REVERT: M 36 TYR cc_start: 0.7099 (m-80) cc_final: 0.6519 (m-80) REVERT: N 58 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7850 (ttt-90) REVERT: O 23 LYS cc_start: 0.7854 (tppt) cc_final: 0.7580 (tppt) REVERT: O 46 GLU cc_start: 0.6226 (pt0) cc_final: 0.5958 (tt0) REVERT: O 48 MET cc_start: 0.7608 (ttm) cc_final: 0.7249 (ttt) REVERT: O 97 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7186 (mm-30) outliers start: 78 outliers final: 53 residues processed: 387 average time/residue: 0.1215 time to fit residues: 75.3658 Evaluate side-chains 378 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 37 GLN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 ASN 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 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 82 ASN 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 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 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 E residue 645 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 24 ARG 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 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 80 ASN 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 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 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 Chi-restraints excluded: chain O residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 167 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 85 optimal weight: 0.0970 chunk 180 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** D 417 GLN ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN J 80 ASN M 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.166594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.138935 restraints weight = 33465.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.142762 restraints weight = 17241.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.145295 restraints weight = 10653.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.146923 restraints weight = 7574.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.147873 restraints weight = 5969.348| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20718 Z= 0.124 Angle : 0.622 12.391 28206 Z= 0.318 Chirality : 0.045 0.178 3261 Planarity : 0.004 0.048 3519 Dihedral : 5.007 31.720 3678 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.07 % Allowed : 15.36 % Favored : 81.56 % 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: -0.05 (0.17), residues: 2427 helix: 1.26 (0.26), residues: 441 sheet: 0.85 (0.22), residues: 585 loop : -0.88 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 54 TYR 0.036 0.002 TYR M 49 PHE 0.013 0.001 PHE J 53 TRP 0.033 0.001 TRP H 36 HIS 0.005 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00282 (20637) covalent geometry : angle 0.60938 (27996) SS BOND : bond 0.00254 ( 33) SS BOND : angle 1.33180 ( 66) hydrogen bonds : bond 0.03726 ( 807) hydrogen bonds : angle 5.20926 ( 2142) link_ALPHA1-2 : bond 0.00080 ( 3) link_ALPHA1-2 : angle 2.41510 ( 9) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 1.56615 ( 9) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 1.90881 ( 27) link_NAG-ASN : bond 0.00146 ( 33) link_NAG-ASN : angle 1.48414 ( 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 415 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 349 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7968 (mtm) cc_final: 0.7739 (mtm) REVERT: A 446 SER cc_start: 0.8833 (m) cc_final: 0.8112 (p) REVERT: A 475 MET cc_start: 0.7528 (mmt) cc_final: 0.7289 (mmm) REVERT: L 89 GLN cc_start: 0.5291 (tt0) cc_final: 0.4964 (tt0) REVERT: C 94 GLN cc_start: 0.6225 (tp40) cc_final: 0.5965 (tp40) REVERT: H 3 GLN cc_start: 0.8352 (pm20) cc_final: 0.8142 (pm20) REVERT: H 39 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6649 (tp-100) REVERT: H 91 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5561 (p90) REVERT: D 64 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6635 (tt0) REVERT: D 475 MET cc_start: 0.7261 (mmm) cc_final: 0.6734 (mmm) REVERT: E 565 MET cc_start: 0.7090 (ptm) cc_final: 0.6800 (ttp) REVERT: E 567 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7048 (tp40) REVERT: E 629 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7104 (mmm) REVERT: G 54 ARG cc_start: 0.8373 (mtp180) cc_final: 0.8083 (mtp180) REVERT: G 58 ARG cc_start: 0.7998 (ttt90) cc_final: 0.7740 (ttt90) REVERT: G 80 ASP cc_start: 0.5679 (m-30) cc_final: 0.5175 (t0) REVERT: G 94 GLN cc_start: 0.5978 (tp40) cc_final: 0.5510 (tp40) REVERT: I 46 GLU cc_start: 0.6334 (pt0) cc_final: 0.5714 (tt0) REVERT: I 72 ASP cc_start: 0.7741 (t0) cc_final: 0.7288 (t0) REVERT: I 91 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.5682 (p90) REVERT: J 64 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6566 (tt0) REVERT: J 82 GLN cc_start: 0.7566 (tp40) cc_final: 0.7198 (tp40) REVERT: J 435 TYR cc_start: 0.7952 (m-80) cc_final: 0.7551 (m-10) REVERT: J 446 SER cc_start: 0.8875 (m) cc_final: 0.8270 (p) REVERT: K 565 MET cc_start: 0.6566 (ptm) cc_final: 0.6020 (ptm) REVERT: K 657 GLU cc_start: 0.7527 (tt0) cc_final: 0.7164 (tt0) REVERT: M 24 ARG cc_start: 0.6871 (ttm110) cc_final: 0.6516 (ttm-80) REVERT: M 36 TYR cc_start: 0.7026 (m-80) cc_final: 0.6563 (m-80) REVERT: N 58 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7925 (ttt90) REVERT: O 48 MET cc_start: 0.7618 (ttm) cc_final: 0.7295 (ttt) REVERT: O 76 SER cc_start: 0.8224 (t) cc_final: 0.7970 (p) REVERT: O 97 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7112 (mm-30) outliers start: 66 outliers final: 46 residues processed: 380 average time/residue: 0.1215 time to fit residues: 73.7597 Evaluate side-chains 366 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 294 ILE Chi-restraints excluded: chain A residue 373 THR 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 37 GLN Chi-restraints excluded: chain C residue 61 LEU 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 54 LEU Chi-restraints excluded: chain H residue 70 THR 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 294 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 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 24 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 86 VAL 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 80 ASN Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 439 ILE 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 O residue 45 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 181 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 132 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 148 optimal weight: 0.0570 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 GLN M 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.165307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.137297 restraints weight = 33861.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.140946 restraints weight = 17817.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.143481 restraints weight = 11221.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.144995 restraints weight = 8015.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.146147 restraints weight = 6403.966| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20718 Z= 0.154 Angle : 0.657 12.268 28206 Z= 0.335 Chirality : 0.046 0.169 3261 Planarity : 0.005 0.046 3519 Dihedral : 5.023 33.922 3678 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.21 % Allowed : 16.20 % Favored : 80.59 % 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: -0.08 (0.17), residues: 2427 helix: 1.23 (0.26), residues: 441 sheet: 0.87 (0.22), residues: 585 loop : -0.92 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 54 TYR 0.034 0.002 TYR M 49 PHE 0.016 0.002 PHE K 522 TRP 0.030 0.001 TRP H 36 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00361 (20637) covalent geometry : angle 0.64476 (27996) SS BOND : bond 0.00348 ( 33) SS BOND : angle 1.37241 ( 66) hydrogen bonds : bond 0.03793 ( 807) hydrogen bonds : angle 5.20327 ( 2142) link_ALPHA1-2 : bond 0.00045 ( 3) link_ALPHA1-2 : angle 2.33385 ( 9) link_ALPHA1-3 : bond 0.00945 ( 3) link_ALPHA1-3 : angle 1.75907 ( 9) link_BETA1-4 : bond 0.00259 ( 9) link_BETA1-4 : angle 2.02114 ( 27) link_NAG-ASN : bond 0.00130 ( 33) link_NAG-ASN : angle 1.52389 ( 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 398 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 329 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7992 (mtm) cc_final: 0.7768 (mtm) REVERT: A 446 SER cc_start: 0.8860 (m) cc_final: 0.8119 (p) REVERT: A 475 MET cc_start: 0.7592 (mmt) cc_final: 0.7295 (mmm) REVERT: C 94 GLN cc_start: 0.6188 (tp40) cc_final: 0.5983 (tp40) REVERT: H 3 GLN cc_start: 0.8367 (pm20) cc_final: 0.8126 (pm20) REVERT: H 12 LYS cc_start: 0.5685 (ttmt) cc_final: 0.5481 (ttmt) REVERT: H 39 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6688 (tp-100) REVERT: H 91 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.5644 (p90) REVERT: D 64 GLU cc_start: 0.7638 (tm-30) cc_final: 0.6670 (tt0) REVERT: E 565 MET cc_start: 0.7054 (ptm) cc_final: 0.6560 (ttp) REVERT: E 567 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7152 (tp40) REVERT: E 629 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7001 (mmm) REVERT: G 58 ARG cc_start: 0.8047 (ttt90) cc_final: 0.7779 (ttt90) REVERT: G 80 ASP cc_start: 0.5805 (m-30) cc_final: 0.5324 (t0) REVERT: G 94 GLN cc_start: 0.6453 (tp40) cc_final: 0.6106 (tp40) REVERT: I 46 GLU cc_start: 0.6121 (pt0) cc_final: 0.5780 (tt0) REVERT: I 72 ASP cc_start: 0.7821 (t0) cc_final: 0.7362 (t0) REVERT: I 91 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5340 (p90) REVERT: J 64 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6613 (tt0) REVERT: J 82 GLN cc_start: 0.7652 (tp40) cc_final: 0.7282 (tp40) REVERT: K 565 MET cc_start: 0.6688 (ptm) cc_final: 0.6270 (ttp) REVERT: K 657 GLU cc_start: 0.7541 (tt0) cc_final: 0.7118 (tt0) REVERT: M 24 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6612 (ttm-80) REVERT: M 36 TYR cc_start: 0.7019 (m-80) cc_final: 0.6687 (m-80) REVERT: N 58 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7807 (ttt-90) REVERT: O 23 LYS cc_start: 0.7818 (tppt) cc_final: 0.7514 (tppt) REVERT: O 36 TRP cc_start: 0.7625 (m100) cc_final: 0.7351 (m-10) REVERT: O 43 GLN cc_start: 0.8094 (tp40) cc_final: 0.7787 (tp40) REVERT: O 97 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7146 (mm-30) outliers start: 69 outliers final: 56 residues processed: 365 average time/residue: 0.1242 time to fit residues: 72.7219 Evaluate side-chains 370 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 309 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 294 ILE 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 61 LEU 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 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 294 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 D residue 496 ILE 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 E residue 645 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 10 GLU 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 216 HIS Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 439 ILE Chi-restraints excluded: chain J residue 496 ILE Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 1 GLU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 3 GLN 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 70 THR 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: 8.9990 chunk 222 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN G 33 GLN J 80 ASN J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN M 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.155674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.129017 restraints weight = 34430.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.131880 restraints weight = 19320.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.132999 restraints weight = 11602.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.133689 restraints weight = 10233.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.133938 restraints weight = 9107.294| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 20718 Z= 0.354 Angle : 0.888 12.714 28206 Z= 0.454 Chirality : 0.054 0.242 3261 Planarity : 0.006 0.062 3519 Dihedral : 6.322 45.052 3678 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.54 % Allowed : 16.34 % Favored : 80.12 % 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: -0.74 (0.17), residues: 2427 helix: 0.55 (0.24), residues: 420 sheet: 0.49 (0.23), residues: 582 loop : -1.28 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 54 TYR 0.028 0.003 TYR K 638 PHE 0.024 0.003 PHE D 376 TRP 0.040 0.003 TRP J 45 HIS 0.011 0.002 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00835 (20637) covalent geometry : angle 0.86671 (27996) SS BOND : bond 0.00574 ( 33) SS BOND : angle 1.87873 ( 66) hydrogen bonds : bond 0.05252 ( 807) hydrogen bonds : angle 5.79531 ( 2142) link_ALPHA1-2 : bond 0.00643 ( 3) link_ALPHA1-2 : angle 3.04398 ( 9) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 2.84670 ( 9) link_BETA1-4 : bond 0.00203 ( 9) link_BETA1-4 : angle 2.90297 ( 27) link_NAG-ASN : bond 0.00463 ( 33) link_NAG-ASN : angle 2.40124 ( 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 404 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 328 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7787 (mmt) cc_final: 0.7514 (mmm) REVERT: C 94 GLN cc_start: 0.6671 (tp40) cc_final: 0.6191 (tp40) REVERT: H 3 GLN cc_start: 0.8296 (pm20) cc_final: 0.8052 (pm20) REVERT: H 39 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6711 (tp-100) REVERT: H 91 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.5815 (p90) REVERT: D 64 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7084 (tt0) REVERT: D 381 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7770 (mm-30) REVERT: E 565 MET cc_start: 0.7224 (ptm) cc_final: 0.6971 (ttp) REVERT: E 567 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7398 (tp40) REVERT: E 629 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7173 (mmm) REVERT: G 54 ARG cc_start: 0.8503 (mtp180) cc_final: 0.8093 (mtp180) REVERT: G 58 ARG cc_start: 0.8320 (ttt90) cc_final: 0.8114 (ttt90) REVERT: G 94 GLN cc_start: 0.6669 (tp40) cc_final: 0.6321 (tp40) REVERT: I 46 GLU cc_start: 0.6497 (pt0) cc_final: 0.5916 (tt0) REVERT: I 72 ASP cc_start: 0.8086 (t0) cc_final: 0.7871 (t0) REVERT: I 91 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5449 (p90) REVERT: J 80 ASN cc_start: 0.6731 (OUTLIER) cc_final: 0.6483 (p0) REVERT: J 435 TYR cc_start: 0.8083 (m-80) cc_final: 0.7697 (m-10) REVERT: K 565 MET cc_start: 0.6910 (ptm) cc_final: 0.6585 (ttp) REVERT: K 657 GLU cc_start: 0.7798 (tt0) cc_final: 0.7476 (tt0) REVERT: M 24 ARG cc_start: 0.7004 (ttm110) cc_final: 0.6772 (ttm-80) REVERT: M 36 TYR cc_start: 0.7658 (m-80) cc_final: 0.7320 (m-80) REVERT: N 58 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8003 (ttt90) REVERT: N 74 LEU cc_start: 0.6594 (mt) cc_final: 0.6099 (mt) REVERT: O 23 LYS cc_start: 0.7852 (tppt) cc_final: 0.7488 (tppt) REVERT: O 97 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7456 (mm-30) outliers start: 76 outliers final: 64 residues processed: 378 average time/residue: 0.1234 time to fit residues: 74.9855 Evaluate side-chains 362 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 292 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 294 ILE Chi-restraints excluded: chain A residue 328 GLN 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 644 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 61 LEU 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 54 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 52 LEU 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 D residue 496 ILE 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 E residue 638 TYR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 24 ARG 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 61 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 25 SER 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 54 CYS Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 1 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 60 SER 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 91 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.156216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.129267 restraints weight = 34392.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.133152 restraints weight = 18532.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.134048 restraints weight = 10409.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.134619 restraints weight = 9092.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.134488 restraints weight = 8038.677| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 20718 Z= 0.283 Angle : 1.004 59.194 28206 Z= 0.550 Chirality : 0.052 0.475 3261 Planarity : 0.007 0.141 3519 Dihedral : 6.336 44.717 3678 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.54 % Allowed : 16.90 % Favored : 79.56 % Cbeta Deviations : 0.09 % 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: -0.81 (0.17), residues: 2427 helix: 0.52 (0.24), residues: 420 sheet: 0.42 (0.22), residues: 582 loop : -1.33 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG N 54 TYR 0.028 0.003 TYR M 49 PHE 0.019 0.003 PHE D 376 TRP 0.079 0.003 TRP O 36 HIS 0.007 0.002 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00656 (20637) covalent geometry : angle 0.98505 (27996) SS BOND : bond 0.00777 ( 33) SS BOND : angle 2.08793 ( 66) hydrogen bonds : bond 0.05021 ( 807) hydrogen bonds : angle 5.77951 ( 2142) link_ALPHA1-2 : bond 0.00793 ( 3) link_ALPHA1-2 : angle 3.26434 ( 9) link_ALPHA1-3 : bond 0.01522 ( 3) link_ALPHA1-3 : angle 3.43119 ( 9) link_BETA1-4 : bond 0.00231 ( 9) link_BETA1-4 : angle 2.92149 ( 27) link_NAG-ASN : bond 0.00461 ( 33) link_NAG-ASN : angle 2.36931 ( 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 370 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 294 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7711 (mmt) cc_final: 0.7430 (mmm) REVERT: C 94 GLN cc_start: 0.6672 (tp40) cc_final: 0.6192 (tp40) REVERT: H 3 GLN cc_start: 0.8286 (pm20) cc_final: 0.8040 (pm20) REVERT: H 39 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6686 (tp-100) REVERT: H 91 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.5867 (p90) REVERT: D 64 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7060 (tt0) REVERT: E 565 MET cc_start: 0.7264 (ptm) cc_final: 0.7037 (ttp) REVERT: E 567 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7362 (tp40) REVERT: E 629 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7241 (mmm) REVERT: G 54 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8109 (mtp180) REVERT: G 58 ARG cc_start: 0.8310 (ttt90) cc_final: 0.8104 (ttt90) REVERT: G 94 GLN cc_start: 0.6716 (tp40) cc_final: 0.6351 (tp40) REVERT: I 46 GLU cc_start: 0.6492 (pt0) cc_final: 0.5919 (tt0) REVERT: I 72 ASP cc_start: 0.8261 (t0) cc_final: 0.7850 (t0) REVERT: I 91 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.5444 (p90) REVERT: J 270 ILE cc_start: 0.8617 (mp) cc_final: 0.8291 (mt) REVERT: J 435 TYR cc_start: 0.8062 (m-80) cc_final: 0.7675 (m-10) REVERT: K 565 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6548 (ttp) REVERT: K 657 GLU cc_start: 0.7782 (tt0) cc_final: 0.7461 (tt0) REVERT: M 24 ARG cc_start: 0.7048 (ttm110) cc_final: 0.6804 (ttm-80) REVERT: M 36 TYR cc_start: 0.7665 (m-80) cc_final: 0.7322 (m-80) REVERT: N 58 ARG cc_start: 0.8406 (mtp85) cc_final: 0.7799 (ttt-90) REVERT: N 74 LEU cc_start: 0.6421 (mt) cc_final: 0.6173 (mt) REVERT: O 97 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7427 (mm-30) outliers start: 76 outliers final: 67 residues processed: 341 average time/residue: 0.1225 time to fit residues: 67.1578 Evaluate side-chains 363 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 290 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 328 GLN 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 644 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 61 LEU 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 70 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain D residue 49 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 522 PHE 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 E residue 638 TYR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 52 ILE 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 54 CYS Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 216 HIS Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 564 HIS Chi-restraints excluded: chain K residue 565 MET Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 618 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain M residue 1 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 71 ILE 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 91 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 175 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 5 optimal weight: 0.3980 chunk 168 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** L 100 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 ASN J 363 HIS ** K 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.156131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.128653 restraints weight = 34466.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.131809 restraints weight = 18861.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.133478 restraints weight = 11106.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.133725 restraints weight = 9069.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.134104 restraints weight = 8446.118| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 20718 Z= 0.283 Angle : 1.004 59.194 28206 Z= 0.550 Chirality : 0.052 0.475 3261 Planarity : 0.007 0.141 3519 Dihedral : 6.336 44.717 3678 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.45 % Allowed : 16.90 % Favored : 79.66 % Cbeta Deviations : 0.09 % 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: -0.81 (0.17), residues: 2427 helix: 0.52 (0.24), residues: 420 sheet: 0.42 (0.22), residues: 582 loop : -1.33 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG N 54 TYR 0.028 0.003 TYR M 49 PHE 0.019 0.003 PHE D 376 TRP 0.079 0.003 TRP O 36 HIS 0.007 0.002 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00656 (20637) covalent geometry : angle 0.98505 (27996) SS BOND : bond 0.00885 ( 33) SS BOND : angle 2.12444 ( 66) hydrogen bonds : bond 0.05021 ( 807) hydrogen bonds : angle 5.77951 ( 2142) link_ALPHA1-2 : bond 0.00793 ( 3) link_ALPHA1-2 : angle 3.26434 ( 9) link_ALPHA1-3 : bond 0.01522 ( 3) link_ALPHA1-3 : angle 3.43118 ( 9) link_BETA1-4 : bond 0.00231 ( 9) link_BETA1-4 : angle 2.92149 ( 27) link_NAG-ASN : bond 0.00461 ( 33) link_NAG-ASN : angle 2.36931 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.72 seconds wall clock time: 55 minutes 50.12 seconds (3350.12 seconds total)