Starting phenix.real_space_refine on Thu Mar 5 02:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o8m_70231/03_2026/9o8m_70231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o8m_70231/03_2026/9o8m_70231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o8m_70231/03_2026/9o8m_70231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o8m_70231/03_2026/9o8m_70231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o8m_70231/03_2026/9o8m_70231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o8m_70231/03_2026/9o8m_70231.map" } resolution = 3.79 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= 0.021 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 112 5.16 5 C 11138 2.51 5 N 2984 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 17749 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "B" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 853 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "D" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 853 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "K" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 5 Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 5 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "I" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 5 Chain: "L" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "K" 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: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.66, per 1000 atoms: 0.21 Number of scatterers: 17749 At special positions: 0 Unit cell: (129.808, 133.597, 159.18, 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 112 16.00 O 3515 8.00 N 2984 7.00 C 11138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.04 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.06 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.04 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.05 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.04 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS J 605 " distance=2.04 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.10 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.05 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.12 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.04 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.05 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS L 605 " distance=2.04 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN H 4 " - " MAN H 5 " " MAN Q 4 " - " MAN Q 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA H 3 " - " MAN H 6 " " BMA Q 3 " - " MAN Q 6 " " BMA U 3 " - " MAN U 6 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 2 " NAG-ASN " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 355 " " NAG G 1 " - " ASN K 234 " " NAG H 1 " - " ASN K 262 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 603 " - " ASN I 197 " " NAG I 604 " - " ASN I 234 " " NAG I 605 " - " ASN I 276 " " NAG I 606 " - " ASN I 355 " " NAG I 607 " - " ASN I 392 " " NAG K 601 " - " ASN K 88 " " NAG K 602 " - " ASN K 160 " " NAG K 603 " - " ASN K 197 " " NAG K 604 " - " ASN K 276 " " NAG K 605 " - " ASN K 295 " " NAG K 606 " - " ASN K 339 " " NAG K 607 " - " ASN K 355 " " NAG K 608 " - " ASN K 392 " " NAG M 1 " - " ASN K 448 " " NAG N 1 " - " ASN K 301 " " NAG O 1 " - " ASN K 386 " " NAG P 1 " - " ASN E 234 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 448 " " NAG S 1 " - " ASN E 301 " " NAG T 1 " - " ASN E 386 " " NAG U 1 " - " ASN I 262 " " NAG V 1 " - " ASN I 448 " " NAG W 1 " - " ASN I 301 " " NAG X 1 " - " ASN I 386 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 675.4 milliseconds 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3986 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 39 sheets defined 25.2% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.840A pdb=" N SER B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.850A pdb=" N SER D 29 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'K' and resid 70 through 74 Processing helix chain 'K' and resid 96 through 98 No H-bonds generated for 'chain 'K' and resid 96 through 98' Processing helix chain 'K' and resid 99 through 117 removed outlier: 3.705A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 127 Processing helix chain 'K' and resid 335 through 354 removed outlier: 3.513A pdb=" N LYS K 344 " --> pdb=" O GLU K 340 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS K 352 " --> pdb=" O GLN K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 474 through 481 removed outlier: 4.118A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 Processing helix chain 'J' and resid 531 through 535 Processing helix chain 'J' and resid 536 through 544 Processing helix chain 'J' and resid 570 through 597 Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 626 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 662 removed outlier: 3.547A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.694A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.838A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.166A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 483 " --> pdb=" O TRP E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.603A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 544 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.500A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.875A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.695A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 127 Processing helix chain 'I' and resid 335 through 354 removed outlier: 3.883A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 484 removed outlier: 3.614A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 483 " --> pdb=" O TRP I 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 523 through 528 removed outlier: 3.501A pdb=" N GLY L 527 " --> pdb=" O GLY L 524 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 535 Processing helix chain 'L' and resid 536 through 544 Processing helix chain 'L' and resid 570 through 597 Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 626 Processing helix chain 'L' and resid 627 through 635 removed outlier: 3.551A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE L 635 " --> pdb=" O TRP L 631 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.197A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.874A pdb=" N VAL B 33 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ARG B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP B 35 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.864A pdb=" N ALA C 94 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP C 36 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY C 52 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP C 38 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.864A pdb=" N ALA C 94 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.828A pdb=" N ALA D 10 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU D 116 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA D 12 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D 89 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL D 33 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'D' and resid 94 through 97 Processing sheet with id=AB4, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.467A pdb=" N VAL J 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL K 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR J 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TYR K 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N CYS J 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 45 through 47 removed outlier: 3.580A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 75 through 76 removed outlier: 3.832A pdb=" N VAL K 75 " --> pdb=" O CYS K 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.535A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 169 through 177 removed outlier: 3.812A pdb=" N LYS K 189 " --> pdb=" O CYS K 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 201 through 203 removed outlier: 6.428A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.070A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N ARG K 444 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 11.443A pdb=" N ILE K 294 " --> pdb=" O ARG K 444 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N VAL K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N VAL K 292 " --> pdb=" O VAL K 446 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR K 450 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 271 through 273 removed outlier: 6.969A pdb=" N THR K 450 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N VAL K 292 " --> pdb=" O VAL K 446 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N VAL K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 11.443A pdb=" N ILE K 294 " --> pdb=" O ARG K 444 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N ARG K 444 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE K 358 " --> pdb=" O GLU K 466 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE K 468 " --> pdb=" O ILE K 358 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 301 through 312 removed outlier: 6.904A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN K 315 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.441A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.728A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.824A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.542A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.430A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.606A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.634A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.845A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.449A pdb=" N VAL L 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL I 38 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR L 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR I 40 " --> pdb=" O CYS L 604 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS L 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'I' and resid 75 through 76 removed outlier: 3.929A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.911A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.386A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.727A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.993A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 301 through 312 removed outlier: 3.817A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS I 305 " --> pdb=" O PHE I 320 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE I 320 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3329 1.32 - 1.45: 4725 1.45 - 1.58: 9906 1.58 - 1.70: 0 1.70 - 1.83: 150 Bond restraints: 18110 Sorted by residual: bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.452 0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" NE ARG C 69 " pdb=" CZ ARG C 69 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.10e-02 8.26e+03 7.99e+00 bond pdb=" CB PHE A 81 " pdb=" CG PHE A 81 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 7.98e+00 bond pdb=" N PRO K 253 " pdb=" CA PRO K 253 " ideal model delta sigma weight residual 1.468 1.435 0.033 1.20e-02 6.94e+03 7.71e+00 bond pdb=" NE ARG I 503 " pdb=" CZ ARG I 503 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.51e+00 ... (remaining 18105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 22628 2.08 - 4.17: 1617 4.17 - 6.25: 283 6.25 - 8.33: 49 8.33 - 10.42: 2 Bond angle restraints: 24579 Sorted by residual: angle pdb=" C GLY D 43 " pdb=" N PRO D 44 " pdb=" CA PRO D 44 " ideal model delta sigma weight residual 119.85 128.12 -8.27 1.01e+00 9.80e-01 6.70e+01 angle pdb=" C GLN A 41 " pdb=" N PRO A 42 " pdb=" CA PRO A 42 " ideal model delta sigma weight residual 119.66 125.59 -5.93 7.30e-01 1.88e+00 6.60e+01 angle pdb=" C GLN C 41 " pdb=" N PRO C 42 " pdb=" CA PRO C 42 " ideal model delta sigma weight residual 119.66 125.43 -5.77 7.30e-01 1.88e+00 6.24e+01 angle pdb=" C GLY B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta sigma weight residual 120.03 127.81 -7.78 9.90e-01 1.02e+00 6.17e+01 angle pdb=" C CYS I 239 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " ideal model delta sigma weight residual 119.56 126.96 -7.40 1.02e+00 9.61e-01 5.26e+01 ... (remaining 24574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 11242 21.25 - 42.50: 270 42.50 - 63.75: 67 63.75 - 85.00: 66 85.00 - 106.25: 29 Dihedral angle restraints: 11674 sinusoidal: 5489 harmonic: 6185 Sorted by residual: dihedral pdb=" CB CYS K 119 " pdb=" SG CYS K 119 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.16 40.16 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.69 39.69 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -120.93 34.93 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 11671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.298: 2925 0.298 - 0.596: 13 0.596 - 0.894: 3 0.894 - 1.192: 2 1.192 - 1.490: 2 Chirality restraints: 2945 Sorted by residual: chirality pdb=" C1 FUC G 2 " pdb=" O6 NAG G 1 " pdb=" C2 FUC G 2 " pdb=" O5 FUC G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-02 2.50e+03 1.77e+03 chirality pdb=" C1 FUC P 2 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 2 " pdb=" O5 FUC P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-02 2.50e+03 1.71e+03 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.12e+02 ... (remaining 2942 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN I 234 " -0.057 2.00e-02 2.50e+03 5.81e-02 4.22e+01 pdb=" CG ASN I 234 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN I 234 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN I 234 " 0.089 2.00e-02 2.50e+03 pdb=" C1 NAG I 604 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 88 " 0.050 2.00e-02 2.50e+03 4.99e-02 3.12e+01 pdb=" CG ASN K 88 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN K 88 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN K 88 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " -0.048 2.00e-02 2.50e+03 4.93e-02 3.03e+01 pdb=" CG ASN E 234 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.058 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5522 2.84 - 3.36: 15188 3.36 - 3.87: 28333 3.87 - 4.39: 31693 4.39 - 4.90: 54464 Nonbonded interactions: 135200 Sorted by model distance: nonbonded pdb=" O5 NAG G 1 " pdb=" O6 NAG G 1 " model vdw 2.331 2.432 nonbonded pdb=" OH TYR C 104 " pdb=" OD1 ASP E 321A" model vdw 2.353 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.389 3.040 nonbonded pdb=" O5 NAG P 1 " pdb=" O2 FUC P 2 " model vdw 2.421 3.040 nonbonded pdb=" NE1 TRP A 36 " pdb=" OG SER A 55 " model vdw 2.433 3.120 ... (remaining 135195 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'I' selection = (chain 'K' and resid 33 through 607) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'W' } 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: 4.140 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.900 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 : 0.011 0.091 18212 Z= 0.620 Angle : 1.341 19.248 24848 Z= 0.835 Chirality : 0.090 1.490 2945 Planarity : 0.005 0.041 3032 Dihedral : 13.058 106.255 7577 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.43 % Rotamer: Outliers : 0.16 % Allowed : 0.53 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.18), residues: 2099 helix: 0.07 (0.21), residues: 435 sheet: 1.49 (0.20), residues: 602 loop : 2.97 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 480 TYR 0.024 0.004 TYR A 35 PHE 0.029 0.003 PHE E 320 TRP 0.030 0.006 TRP A 113 HIS 0.002 0.000 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.01084 (18110) covalent geometry : angle 1.23720 (24579) SS BOND : bond 0.02089 ( 37) SS BOND : angle 2.23028 ( 74) hydrogen bonds : bond 0.23541 ( 693) hydrogen bonds : angle 7.41699 ( 1860) link_ALPHA1-2 : bond 0.04502 ( 3) link_ALPHA1-2 : angle 6.99801 ( 9) link_ALPHA1-3 : bond 0.04609 ( 3) link_ALPHA1-3 : angle 4.42360 ( 9) link_ALPHA1-6 : bond 0.03825 ( 3) link_ALPHA1-6 : angle 4.45833 ( 9) link_BETA1-4 : bond 0.04327 ( 18) link_BETA1-4 : angle 7.27978 ( 54) link_BETA1-6 : bond 0.02415 ( 2) link_BETA1-6 : angle 7.53888 ( 6) link_NAG-ASN : bond 0.07063 ( 36) link_NAG-ASN : angle 5.00932 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 548 time to evaluate : 0.533 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: A 31 SER cc_start: 0.7700 (p) cc_final: 0.7340 (t) REVERT: A 92 ASP cc_start: 0.7768 (m-30) cc_final: 0.7521 (m-30) REVERT: D 39 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7254 (mmt90) REVERT: D 67 PHE cc_start: 0.8460 (m-80) cc_final: 0.7988 (m-10) REVERT: K 180 ASP cc_start: 0.7386 (m-30) cc_final: 0.7072 (m-30) REVERT: K 199 SER cc_start: 0.8310 (p) cc_final: 0.8028 (t) REVERT: E 50 THR cc_start: 0.8998 (t) cc_final: 0.8656 (m) REVERT: E 223 PHE cc_start: 0.6882 (m-80) cc_final: 0.6433 (m-80) REVERT: E 475 MET cc_start: 0.7486 (mmm) cc_final: 0.7268 (tpp) REVERT: I 95 MET cc_start: 0.6553 (ttp) cc_final: 0.6334 (ttm) REVERT: I 426 MET cc_start: 0.7880 (tpt) cc_final: 0.7605 (tpt) REVERT: L 575 GLN cc_start: 0.7718 (tt0) cc_final: 0.7353 (mt0) REVERT: L 641 ILE cc_start: 0.7283 (mt) cc_final: 0.6827 (mt) REVERT: L 653 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8087 (tm-30) outliers start: 3 outliers final: 2 residues processed: 549 average time/residue: 0.1239 time to fit residues: 103.8393 Evaluate side-chains 299 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 386 ASN Chi-restraints excluded: chain I residue 386 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 352 HIS K 440 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS F 625 ASN I 114 GLN I 195 ASN I 315 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.227398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.188103 restraints weight = 27721.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.192743 restraints weight = 17310.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195765 restraints weight = 12690.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.197703 restraints weight = 10288.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.198668 restraints weight = 8988.804| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18212 Z= 0.179 Angle : 0.799 17.102 24848 Z= 0.391 Chirality : 0.050 0.511 2945 Planarity : 0.004 0.042 3032 Dihedral : 9.895 78.144 3622 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 0.71 % Favored : 99.19 % Rotamer: Outliers : 2.91 % Allowed : 8.30 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.18), residues: 2099 helix: 2.20 (0.26), residues: 399 sheet: 1.14 (0.18), residues: 739 loop : 2.21 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 327 TYR 0.020 0.002 TYR I 40 PHE 0.025 0.002 PHE C 81 TRP 0.030 0.002 TRP C 49 HIS 0.006 0.001 HIS K 85 Details of bonding type rmsd covalent geometry : bond 0.00368 (18110) covalent geometry : angle 0.72090 (24579) SS BOND : bond 0.00562 ( 37) SS BOND : angle 1.70867 ( 74) hydrogen bonds : bond 0.07799 ( 693) hydrogen bonds : angle 5.77755 ( 1860) link_ALPHA1-2 : bond 0.00559 ( 3) link_ALPHA1-2 : angle 2.19784 ( 9) link_ALPHA1-3 : bond 0.01681 ( 3) link_ALPHA1-3 : angle 1.01961 ( 9) link_ALPHA1-6 : bond 0.00551 ( 3) link_ALPHA1-6 : angle 1.39987 ( 9) link_BETA1-4 : bond 0.00704 ( 18) link_BETA1-4 : angle 2.87692 ( 54) link_BETA1-6 : bond 0.02272 ( 2) link_BETA1-6 : angle 4.59427 ( 6) link_NAG-ASN : bond 0.00781 ( 36) link_NAG-ASN : angle 4.53662 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 0.500 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 13 LYS cc_start: 0.8898 (mttp) cc_final: 0.8313 (mmtt) REVERT: A 89 THR cc_start: 0.8159 (t) cc_final: 0.7421 (p) REVERT: A 92 ASP cc_start: 0.7769 (m-30) cc_final: 0.7224 (m-30) REVERT: B 88 GLU cc_start: 0.7558 (tp30) cc_final: 0.7137 (tp30) REVERT: C 49 TRP cc_start: 0.6950 (t60) cc_final: 0.6707 (t60) REVERT: D 39 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7615 (mmt90) REVERT: D 67 PHE cc_start: 0.8342 (m-80) cc_final: 0.7661 (m-80) REVERT: K 100 MET cc_start: 0.6759 (mtp) cc_final: 0.6538 (mtm) REVERT: K 180 ASP cc_start: 0.7767 (m-30) cc_final: 0.7174 (m-30) REVERT: K 207 LYS cc_start: 0.7763 (mttt) cc_final: 0.7379 (tttt) REVERT: E 50 THR cc_start: 0.9020 (t) cc_final: 0.8623 (m) REVERT: E 95 MET cc_start: 0.7006 (ptm) cc_final: 0.6621 (ptm) REVERT: E 223 PHE cc_start: 0.7014 (m-80) cc_final: 0.6263 (m-80) REVERT: F 610 TRP cc_start: 0.6348 (t-100) cc_final: 0.6098 (t-100) REVERT: I 95 MET cc_start: 0.6763 (ttp) cc_final: 0.6514 (ttt) REVERT: I 110 SER cc_start: 0.7953 (m) cc_final: 0.7348 (t) REVERT: I 150 MET cc_start: 0.6372 (mmm) cc_final: 0.6138 (mmm) REVERT: I 328 MET cc_start: 0.7475 (ttp) cc_final: 0.6925 (ptt) REVERT: L 535 MET cc_start: 0.7744 (mmt) cc_final: 0.7231 (mmp) REVERT: L 575 GLN cc_start: 0.7712 (tt0) cc_final: 0.7186 (mt0) REVERT: L 621 GLU cc_start: 0.6080 (mp0) cc_final: 0.5875 (mm-30) outliers start: 55 outliers final: 27 residues processed: 364 average time/residue: 0.1293 time to fit residues: 71.6009 Evaluate side-chains 311 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain I residue 45 TRP Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain L residue 519 SER Chi-restraints excluded: chain L residue 536 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 77 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN D 6 GLN D 36 HIS J 591 GLN E 203 GLN E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN I 195 ASN I 287 GLN L 607 ASN L 630 GLN ** L 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.216266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.181830 restraints weight = 28423.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.182438 restraints weight = 24986.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.184873 restraints weight = 19606.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185316 restraints weight = 14744.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.186014 restraints weight = 14301.156| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18212 Z= 0.250 Angle : 0.825 13.534 24848 Z= 0.409 Chirality : 0.053 0.485 2945 Planarity : 0.005 0.058 3032 Dihedral : 8.780 70.862 3618 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.43 % Favored : 98.48 % Rotamer: Outliers : 3.44 % Allowed : 10.41 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2099 helix: 1.81 (0.26), residues: 402 sheet: 0.58 (0.18), residues: 728 loop : 1.23 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 100 TYR 0.020 0.002 TYR A 33 PHE 0.031 0.003 PHE E 376 TRP 0.023 0.002 TRP C 36 HIS 0.014 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00577 (18110) covalent geometry : angle 0.76185 (24579) SS BOND : bond 0.00563 ( 37) SS BOND : angle 1.70378 ( 74) hydrogen bonds : bond 0.06560 ( 693) hydrogen bonds : angle 5.68249 ( 1860) link_ALPHA1-2 : bond 0.00467 ( 3) link_ALPHA1-2 : angle 2.08931 ( 9) link_ALPHA1-3 : bond 0.01578 ( 3) link_ALPHA1-3 : angle 0.61077 ( 9) link_ALPHA1-6 : bond 0.00597 ( 3) link_ALPHA1-6 : angle 1.49102 ( 9) link_BETA1-4 : bond 0.00565 ( 18) link_BETA1-4 : angle 2.60808 ( 54) link_BETA1-6 : bond 0.02305 ( 2) link_BETA1-6 : angle 4.17880 ( 6) link_NAG-ASN : bond 0.00919 ( 36) link_NAG-ASN : angle 4.17542 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 0.622 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: A 13 LYS cc_start: 0.8939 (mttp) cc_final: 0.8397 (mmtt) REVERT: A 78 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7782 (ttmm) REVERT: A 92 ASP cc_start: 0.7893 (m-30) cc_final: 0.7570 (m-30) REVERT: C 49 TRP cc_start: 0.7083 (t60) cc_final: 0.6846 (t60) REVERT: D 35 TRP cc_start: 0.8055 (m100) cc_final: 0.7762 (m100) REVERT: D 67 PHE cc_start: 0.7856 (m-80) cc_final: 0.7126 (m-10) REVERT: K 180 ASP cc_start: 0.7827 (m-30) cc_final: 0.7515 (m-30) REVERT: K 199 SER cc_start: 0.8891 (p) cc_final: 0.8491 (t) REVERT: K 207 LYS cc_start: 0.7754 (mttt) cc_final: 0.7440 (tttt) REVERT: K 475 MET cc_start: 0.8351 (mmm) cc_final: 0.7865 (mmt) REVERT: E 50 THR cc_start: 0.9141 (t) cc_final: 0.8654 (m) REVERT: E 223 PHE cc_start: 0.7606 (m-80) cc_final: 0.6927 (m-80) REVERT: I 95 MET cc_start: 0.6949 (ttp) cc_final: 0.6610 (ttm) REVERT: I 180 ASP cc_start: 0.8109 (m-30) cc_final: 0.7890 (t0) REVERT: I 342 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6662 (tt) REVERT: L 575 GLN cc_start: 0.7594 (tt0) cc_final: 0.7072 (mt0) REVERT: L 584 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: L 591 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6476 (mp10) REVERT: L 621 GLU cc_start: 0.6339 (mp0) cc_final: 0.6008 (mm-30) outliers start: 65 outliers final: 42 residues processed: 336 average time/residue: 0.1258 time to fit residues: 65.1582 Evaluate side-chains 289 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 591 GLN Chi-restraints excluded: chain L residue 599 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 28 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 330 HIS E 183 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS I 287 GLN ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 607 ASN L 630 GLN ** L 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 653 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.211761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.176912 restraints weight = 28431.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.178819 restraints weight = 22523.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.180369 restraints weight = 17579.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.180889 restraints weight = 14199.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.181481 restraints weight = 13017.139| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18212 Z= 0.237 Angle : 0.789 12.030 24848 Z= 0.388 Chirality : 0.051 0.397 2945 Planarity : 0.005 0.048 3032 Dihedral : 8.327 64.041 3618 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 3.49 % Allowed : 12.58 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.18), residues: 2099 helix: 1.70 (0.27), residues: 402 sheet: 0.48 (0.19), residues: 688 loop : 0.61 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 100 TYR 0.017 0.002 TYR I 39 PHE 0.028 0.003 PHE E 320 TRP 0.016 0.002 TRP K 479 HIS 0.005 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00549 (18110) covalent geometry : angle 0.73257 (24579) SS BOND : bond 0.00450 ( 37) SS BOND : angle 1.45782 ( 74) hydrogen bonds : bond 0.05953 ( 693) hydrogen bonds : angle 5.54174 ( 1860) link_ALPHA1-2 : bond 0.00375 ( 3) link_ALPHA1-2 : angle 1.99772 ( 9) link_ALPHA1-3 : bond 0.01587 ( 3) link_ALPHA1-3 : angle 0.55590 ( 9) link_ALPHA1-6 : bond 0.00768 ( 3) link_ALPHA1-6 : angle 1.56846 ( 9) link_BETA1-4 : bond 0.00584 ( 18) link_BETA1-4 : angle 2.37010 ( 54) link_BETA1-6 : bond 0.02344 ( 2) link_BETA1-6 : angle 4.32917 ( 6) link_NAG-ASN : bond 0.00690 ( 36) link_NAG-ASN : angle 3.89761 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 0.833 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 13 LYS cc_start: 0.8937 (mttp) cc_final: 0.8209 (mmtt) REVERT: A 78 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7612 (ttmm) REVERT: A 92 ASP cc_start: 0.7990 (m-30) cc_final: 0.7647 (m-30) REVERT: A 111 ASP cc_start: 0.7240 (m-30) cc_final: 0.6888 (m-30) REVERT: B 88 GLU cc_start: 0.7953 (tp30) cc_final: 0.7569 (tp30) REVERT: C 49 TRP cc_start: 0.7071 (t60) cc_final: 0.6602 (t60) REVERT: D 35 TRP cc_start: 0.8252 (m100) cc_final: 0.7996 (m100) REVERT: D 67 PHE cc_start: 0.7841 (m-80) cc_final: 0.7074 (m-10) REVERT: K 180 ASP cc_start: 0.7752 (m-30) cc_final: 0.7399 (m-30) REVERT: K 199 SER cc_start: 0.8973 (p) cc_final: 0.8450 (m) REVERT: K 475 MET cc_start: 0.8340 (mmm) cc_final: 0.7900 (mmt) REVERT: I 121 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7947 (tptm) REVERT: I 267 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: I 342 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6620 (tt) REVERT: L 575 GLN cc_start: 0.7531 (tt0) cc_final: 0.6918 (mt0) REVERT: L 584 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: L 610 TRP cc_start: 0.6938 (t-100) cc_final: 0.6664 (t-100) REVERT: L 621 GLU cc_start: 0.6407 (mp0) cc_final: 0.6127 (mm-30) REVERT: L 649 SER cc_start: 0.8676 (m) cc_final: 0.8045 (t) outliers start: 66 outliers final: 51 residues processed: 324 average time/residue: 0.1236 time to fit residues: 62.4156 Evaluate side-chains 296 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 365 SER Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 469 ARG Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 642 ILE Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 628 TRP Chi-restraints excluded: chain L residue 637 ASN Chi-restraints excluded: chain L residue 653 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 209 optimal weight: 9.9990 chunk 182 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 114 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN D 6 GLN K 425 ASN F 540 GLN I 293 GLN L 607 ASN L 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.215934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.181177 restraints weight = 28327.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.183244 restraints weight = 21897.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.184878 restraints weight = 17269.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.185531 restraints weight = 13044.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.186190 restraints weight = 12533.790| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18212 Z= 0.137 Angle : 0.683 11.348 24848 Z= 0.332 Chirality : 0.046 0.260 2945 Planarity : 0.004 0.043 3032 Dihedral : 7.628 59.403 3618 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.07 % Allowed : 14.53 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2099 helix: 1.98 (0.27), residues: 402 sheet: 0.71 (0.19), residues: 683 loop : 0.58 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100 TYR 0.026 0.002 TYR F 638 PHE 0.031 0.002 PHE E 320 TRP 0.027 0.001 TRP F 610 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00298 (18110) covalent geometry : angle 0.62977 (24579) SS BOND : bond 0.00248 ( 37) SS BOND : angle 1.20138 ( 74) hydrogen bonds : bond 0.05058 ( 693) hydrogen bonds : angle 5.29739 ( 1860) link_ALPHA1-2 : bond 0.00301 ( 3) link_ALPHA1-2 : angle 1.98931 ( 9) link_ALPHA1-3 : bond 0.01566 ( 3) link_ALPHA1-3 : angle 0.67748 ( 9) link_ALPHA1-6 : bond 0.00832 ( 3) link_ALPHA1-6 : angle 1.60184 ( 9) link_BETA1-4 : bond 0.00546 ( 18) link_BETA1-4 : angle 1.98458 ( 54) link_BETA1-6 : bond 0.02873 ( 2) link_BETA1-6 : angle 4.51406 ( 6) link_NAG-ASN : bond 0.00673 ( 36) link_NAG-ASN : angle 3.54151 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.678 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: A 13 LYS cc_start: 0.8740 (mttp) cc_final: 0.8126 (mmtt) REVERT: A 78 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7421 (ttmm) REVERT: A 92 ASP cc_start: 0.7962 (m-30) cc_final: 0.7584 (m-30) REVERT: B 88 GLU cc_start: 0.7915 (tp30) cc_final: 0.7640 (tp30) REVERT: D 67 PHE cc_start: 0.7938 (m-80) cc_final: 0.7093 (m-10) REVERT: K 180 ASP cc_start: 0.7752 (m-30) cc_final: 0.7407 (m-30) REVERT: K 199 SER cc_start: 0.8976 (p) cc_final: 0.8383 (m) REVERT: K 234 ASN cc_start: 0.4943 (OUTLIER) cc_final: 0.4527 (p0) REVERT: K 475 MET cc_start: 0.8313 (mmm) cc_final: 0.7936 (mmt) REVERT: E 282 LYS cc_start: 0.6830 (tptt) cc_final: 0.6561 (tptt) REVERT: F 530 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5789 (mtt) REVERT: I 121 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7813 (tptm) REVERT: I 150 MET cc_start: 0.6565 (mmm) cc_final: 0.6211 (mmm) REVERT: I 328 MET cc_start: 0.7445 (ttp) cc_final: 0.6757 (ptt) REVERT: I 342 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6408 (tt) REVERT: L 575 GLN cc_start: 0.7526 (tt0) cc_final: 0.6881 (mt0) REVERT: L 584 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: L 610 TRP cc_start: 0.6948 (t-100) cc_final: 0.6624 (t-100) REVERT: L 621 GLU cc_start: 0.6527 (mp0) cc_final: 0.6287 (mm-30) REVERT: L 649 SER cc_start: 0.8703 (m) cc_final: 0.8157 (t) REVERT: L 655 LYS cc_start: 0.7438 (tptp) cc_final: 0.7192 (pttt) REVERT: L 658 GLN cc_start: 0.6455 (tm-30) cc_final: 0.6071 (pp30) outliers start: 58 outliers final: 44 residues processed: 310 average time/residue: 0.1263 time to fit residues: 60.7461 Evaluate side-chains 296 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 365 SER Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 469 ARG Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 642 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 386 ASN Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 591 GLN Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 637 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 198 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 chunk 129 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN D 37 GLN F 630 GLN L 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.216442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.180239 restraints weight = 28047.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.183586 restraints weight = 21776.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.185488 restraints weight = 14614.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185597 restraints weight = 11397.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.185916 restraints weight = 11228.136| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18212 Z= 0.141 Angle : 0.675 10.883 24848 Z= 0.329 Chirality : 0.046 0.251 2945 Planarity : 0.004 0.042 3032 Dihedral : 7.318 57.578 3618 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.70 % Allowed : 14.96 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 2099 helix: 2.05 (0.27), residues: 402 sheet: 0.64 (0.19), residues: 685 loop : 0.52 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.029 0.002 TYR C 33 PHE 0.027 0.002 PHE E 320 TRP 0.032 0.002 TRP C 49 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00316 (18110) covalent geometry : angle 0.62631 (24579) SS BOND : bond 0.00262 ( 37) SS BOND : angle 1.17431 ( 74) hydrogen bonds : bond 0.04737 ( 693) hydrogen bonds : angle 5.17677 ( 1860) link_ALPHA1-2 : bond 0.00273 ( 3) link_ALPHA1-2 : angle 1.90194 ( 9) link_ALPHA1-3 : bond 0.01528 ( 3) link_ALPHA1-3 : angle 0.69911 ( 9) link_ALPHA1-6 : bond 0.00887 ( 3) link_ALPHA1-6 : angle 1.68283 ( 9) link_BETA1-4 : bond 0.00525 ( 18) link_BETA1-4 : angle 1.87709 ( 54) link_BETA1-6 : bond 0.02866 ( 2) link_BETA1-6 : angle 4.37068 ( 6) link_NAG-ASN : bond 0.00550 ( 36) link_NAG-ASN : angle 3.35528 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 265 time to evaluate : 0.732 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: A 13 LYS cc_start: 0.8656 (mttp) cc_final: 0.8211 (mmtt) REVERT: A 78 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7622 (ttmm) REVERT: A 89 THR cc_start: 0.8276 (t) cc_final: 0.7602 (p) REVERT: A 92 ASP cc_start: 0.8048 (m-30) cc_final: 0.7686 (m-30) REVERT: B 88 GLU cc_start: 0.7850 (tp30) cc_final: 0.7635 (tp30) REVERT: D 24 LEU cc_start: 0.8660 (mp) cc_final: 0.8356 (mp) REVERT: D 39 ARG cc_start: 0.6096 (mmt-90) cc_final: 0.5668 (mmt-90) REVERT: D 67 PHE cc_start: 0.7867 (m-80) cc_final: 0.6905 (m-10) REVERT: K 180 ASP cc_start: 0.7640 (m-30) cc_final: 0.7355 (m-30) REVERT: K 199 SER cc_start: 0.8960 (p) cc_final: 0.8371 (m) REVERT: K 234 ASN cc_start: 0.5275 (OUTLIER) cc_final: 0.4794 (p0) REVERT: K 282 LYS cc_start: 0.7785 (mmtt) cc_final: 0.7280 (tptt) REVERT: K 475 MET cc_start: 0.8293 (mmm) cc_final: 0.7951 (mmt) REVERT: J 523 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6835 (tt) REVERT: E 84 ILE cc_start: 0.6570 (mt) cc_final: 0.6358 (mt) REVERT: F 530 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5865 (mtt) REVERT: F 656 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8637 (t0) REVERT: I 121 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7821 (tptm) REVERT: I 150 MET cc_start: 0.6673 (mmm) cc_final: 0.6314 (mmm) REVERT: I 328 MET cc_start: 0.7349 (ttp) cc_final: 0.6793 (ptt) REVERT: I 342 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6406 (tt) REVERT: I 485 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7504 (mtmt) REVERT: L 575 GLN cc_start: 0.7288 (tt0) cc_final: 0.6674 (mt0) REVERT: L 584 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: L 649 SER cc_start: 0.8650 (m) cc_final: 0.8105 (t) REVERT: L 658 GLN cc_start: 0.6294 (tm-30) cc_final: 0.6054 (pp30) outliers start: 70 outliers final: 54 residues processed: 314 average time/residue: 0.1221 time to fit residues: 59.1563 Evaluate side-chains 318 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 257 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 386 ASN Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 485 LYS Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 591 GLN Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 637 ASN Chi-restraints excluded: chain L residue 653 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 137 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 149 ASN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN I 287 GLN I 425 ASN L 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.211560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.177178 restraints weight = 28579.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177776 restraints weight = 23409.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.179365 restraints weight = 20615.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180016 restraints weight = 15526.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.180330 restraints weight = 14393.051| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18212 Z= 0.208 Angle : 0.739 10.788 24848 Z= 0.364 Chirality : 0.048 0.263 2945 Planarity : 0.004 0.047 3032 Dihedral : 7.464 54.463 3618 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.23 % Allowed : 15.12 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2099 helix: 1.56 (0.26), residues: 414 sheet: 0.46 (0.19), residues: 698 loop : 0.26 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 100 TYR 0.054 0.002 TYR C 33 PHE 0.024 0.003 PHE E 376 TRP 0.032 0.002 TRP C 49 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00487 (18110) covalent geometry : angle 0.69346 (24579) SS BOND : bond 0.00402 ( 37) SS BOND : angle 1.28055 ( 74) hydrogen bonds : bond 0.05136 ( 693) hydrogen bonds : angle 5.30972 ( 1860) link_ALPHA1-2 : bond 0.00307 ( 3) link_ALPHA1-2 : angle 1.89424 ( 9) link_ALPHA1-3 : bond 0.01631 ( 3) link_ALPHA1-3 : angle 0.65000 ( 9) link_ALPHA1-6 : bond 0.00906 ( 3) link_ALPHA1-6 : angle 1.70723 ( 9) link_BETA1-4 : bond 0.00560 ( 18) link_BETA1-4 : angle 2.01733 ( 54) link_BETA1-6 : bond 0.02652 ( 2) link_BETA1-6 : angle 4.26249 ( 6) link_NAG-ASN : bond 0.00568 ( 36) link_NAG-ASN : angle 3.39189 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 252 time to evaluate : 0.641 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: A 13 LYS cc_start: 0.8732 (mttp) cc_final: 0.8378 (mmtt) REVERT: A 67 LYS cc_start: 0.8313 (tttt) cc_final: 0.7822 (tptt) REVERT: A 78 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7628 (ttmm) REVERT: A 89 THR cc_start: 0.8350 (t) cc_final: 0.7921 (p) REVERT: A 92 ASP cc_start: 0.8111 (m-30) cc_final: 0.7807 (t0) REVERT: B 88 GLU cc_start: 0.7779 (tp30) cc_final: 0.7564 (tp30) REVERT: C 38 TRP cc_start: 0.7501 (OUTLIER) cc_final: 0.6033 (m-90) REVERT: D 24 LEU cc_start: 0.8620 (mp) cc_final: 0.8309 (mp) REVERT: D 46 PHE cc_start: 0.7263 (t80) cc_final: 0.6742 (t80) REVERT: D 67 PHE cc_start: 0.7738 (m-80) cc_final: 0.6935 (m-80) REVERT: K 180 ASP cc_start: 0.7703 (m-30) cc_final: 0.7391 (m-30) REVERT: K 199 SER cc_start: 0.9039 (p) cc_final: 0.8450 (m) REVERT: K 234 ASN cc_start: 0.5570 (OUTLIER) cc_final: 0.5047 (p0) REVERT: K 475 MET cc_start: 0.8294 (mmm) cc_final: 0.7964 (mmt) REVERT: E 84 ILE cc_start: 0.7001 (mt) cc_final: 0.6783 (mt) REVERT: E 254 VAL cc_start: 0.8211 (t) cc_final: 0.7954 (m) REVERT: F 655 LYS cc_start: 0.8520 (ptmm) cc_final: 0.8261 (pptt) REVERT: I 47 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7818 (p0) REVERT: I 121 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7792 (tptm) REVERT: I 213 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8347 (mm) REVERT: I 342 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6561 (tt) REVERT: I 485 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7332 (mtpt) REVERT: L 575 GLN cc_start: 0.7312 (tt0) cc_final: 0.6689 (mt0) REVERT: L 584 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: L 610 TRP cc_start: 0.6896 (t-100) cc_final: 0.6512 (t-100) REVERT: L 653 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7539 (tm-30) outliers start: 80 outliers final: 60 residues processed: 313 average time/residue: 0.1230 time to fit residues: 59.8779 Evaluate side-chains 308 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 240 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain K residue 53 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 365 SER Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 469 ARG Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 386 ASN Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 485 LYS Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 591 GLN Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 628 TRP Chi-restraints excluded: chain L residue 637 ASN Chi-restraints excluded: chain L residue 653 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 138 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 105 optimal weight: 0.0070 chunk 181 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 167 optimal weight: 0.0670 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN L 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.215253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.181142 restraints weight = 28225.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.183384 restraints weight = 21985.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.184744 restraints weight = 17884.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185081 restraints weight = 13129.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.186131 restraints weight = 12509.274| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18212 Z= 0.139 Angle : 0.681 10.876 24848 Z= 0.333 Chirality : 0.046 0.248 2945 Planarity : 0.004 0.041 3032 Dihedral : 7.003 52.990 3618 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.49 % Allowed : 15.64 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2099 helix: 1.67 (0.26), residues: 414 sheet: 0.53 (0.19), residues: 683 loop : 0.23 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 100 TYR 0.046 0.002 TYR C 33 PHE 0.027 0.002 PHE E 320 TRP 0.038 0.002 TRP C 49 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00312 (18110) covalent geometry : angle 0.63529 (24579) SS BOND : bond 0.00246 ( 37) SS BOND : angle 1.13507 ( 74) hydrogen bonds : bond 0.04524 ( 693) hydrogen bonds : angle 5.16413 ( 1860) link_ALPHA1-2 : bond 0.00222 ( 3) link_ALPHA1-2 : angle 1.91616 ( 9) link_ALPHA1-3 : bond 0.01487 ( 3) link_ALPHA1-3 : angle 0.72760 ( 9) link_ALPHA1-6 : bond 0.00937 ( 3) link_ALPHA1-6 : angle 1.70751 ( 9) link_BETA1-4 : bond 0.00533 ( 18) link_BETA1-4 : angle 1.77241 ( 54) link_BETA1-6 : bond 0.02927 ( 2) link_BETA1-6 : angle 4.53630 ( 6) link_NAG-ASN : bond 0.00541 ( 36) link_NAG-ASN : angle 3.25109 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 0.696 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 13 LYS cc_start: 0.8799 (mttp) cc_final: 0.8404 (mmtt) REVERT: A 62 TYR cc_start: 0.6689 (m-80) cc_final: 0.6486 (m-80) REVERT: A 67 LYS cc_start: 0.8269 (tttt) cc_final: 0.7992 (tptp) REVERT: A 78 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7602 (ttmm) REVERT: A 89 THR cc_start: 0.8294 (t) cc_final: 0.7881 (p) REVERT: A 92 ASP cc_start: 0.8088 (m-30) cc_final: 0.7753 (t0) REVERT: C 38 TRP cc_start: 0.7489 (OUTLIER) cc_final: 0.6142 (m-90) REVERT: D 24 LEU cc_start: 0.8587 (mp) cc_final: 0.8277 (mp) REVERT: K 180 ASP cc_start: 0.7694 (m-30) cc_final: 0.7391 (m-30) REVERT: K 199 SER cc_start: 0.9027 (p) cc_final: 0.8374 (m) REVERT: K 234 ASN cc_start: 0.5393 (OUTLIER) cc_final: 0.4893 (p0) REVERT: K 282 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7307 (tptt) REVERT: K 475 MET cc_start: 0.8279 (mmm) cc_final: 0.7955 (mmt) REVERT: E 254 VAL cc_start: 0.8280 (t) cc_final: 0.8061 (p) REVERT: E 258 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8215 (mm-40) REVERT: E 482 GLU cc_start: 0.6669 (mp0) cc_final: 0.6394 (mp0) REVERT: F 655 LYS cc_start: 0.8486 (ptmm) cc_final: 0.8283 (pptt) REVERT: I 121 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7784 (tptm) REVERT: I 213 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8273 (mm) REVERT: I 342 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6481 (tt) REVERT: L 575 GLN cc_start: 0.7224 (tt0) cc_final: 0.6657 (mt0) REVERT: L 584 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: L 610 TRP cc_start: 0.6913 (t-100) cc_final: 0.6552 (t-100) REVERT: L 645 LEU cc_start: 0.8497 (mt) cc_final: 0.7978 (tp) REVERT: L 648 GLU cc_start: 0.7783 (pp20) cc_final: 0.7469 (pp20) outliers start: 66 outliers final: 54 residues processed: 313 average time/residue: 0.1209 time to fit residues: 58.3596 Evaluate side-chains 308 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 365 SER Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 469 ARG Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 386 ASN Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 591 GLN Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 628 TRP Chi-restraints excluded: chain L residue 637 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 185 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 128 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 591 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.214611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179955 restraints weight = 28473.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.181764 restraints weight = 22470.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.183361 restraints weight = 17869.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183789 restraints weight = 13827.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.184165 restraints weight = 12872.121| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18212 Z= 0.148 Angle : 0.719 25.353 24848 Z= 0.343 Chirality : 0.046 0.249 2945 Planarity : 0.004 0.044 3032 Dihedral : 6.915 51.186 3618 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.44 % Allowed : 15.86 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 2099 helix: 1.88 (0.27), residues: 402 sheet: 0.46 (0.19), residues: 691 loop : 0.22 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.045 0.002 TYR C 33 PHE 0.024 0.002 PHE E 320 TRP 0.039 0.002 TRP C 49 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00338 (18110) covalent geometry : angle 0.64479 (24579) SS BOND : bond 0.00256 ( 37) SS BOND : angle 1.13914 ( 74) hydrogen bonds : bond 0.04497 ( 693) hydrogen bonds : angle 5.10686 ( 1860) link_ALPHA1-2 : bond 0.00234 ( 3) link_ALPHA1-2 : angle 1.86999 ( 9) link_ALPHA1-3 : bond 0.01537 ( 3) link_ALPHA1-3 : angle 0.78995 ( 9) link_ALPHA1-6 : bond 0.00953 ( 3) link_ALPHA1-6 : angle 1.71790 ( 9) link_BETA1-4 : bond 0.00537 ( 18) link_BETA1-4 : angle 1.75952 ( 54) link_BETA1-6 : bond 0.02834 ( 2) link_BETA1-6 : angle 4.35058 ( 6) link_NAG-ASN : bond 0.00511 ( 36) link_NAG-ASN : angle 4.49363 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 0.588 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: A 13 LYS cc_start: 0.8714 (mttp) cc_final: 0.8329 (mmtt) REVERT: A 67 LYS cc_start: 0.8295 (tttt) cc_final: 0.8020 (tptp) REVERT: A 78 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7601 (ttmm) REVERT: A 89 THR cc_start: 0.8189 (t) cc_final: 0.7766 (p) REVERT: A 92 ASP cc_start: 0.8067 (m-30) cc_final: 0.7755 (t0) REVERT: B 88 GLU cc_start: 0.7894 (tp30) cc_final: 0.7602 (tp30) REVERT: C 38 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.6271 (m-90) REVERT: D 24 LEU cc_start: 0.8645 (mp) cc_final: 0.8334 (mp) REVERT: K 180 ASP cc_start: 0.7700 (m-30) cc_final: 0.7107 (m-30) REVERT: K 199 SER cc_start: 0.9066 (p) cc_final: 0.8392 (m) REVERT: K 234 ASN cc_start: 0.5383 (OUTLIER) cc_final: 0.4899 (p0) REVERT: K 475 MET cc_start: 0.8267 (mmm) cc_final: 0.7923 (mmt) REVERT: J 593 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5881 (tp) REVERT: E 254 VAL cc_start: 0.8452 (t) cc_final: 0.8246 (p) REVERT: E 482 GLU cc_start: 0.6682 (mp0) cc_final: 0.6372 (mp0) REVERT: F 655 LYS cc_start: 0.8475 (ptmm) cc_final: 0.8266 (pptt) REVERT: I 121 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7752 (tptm) REVERT: I 213 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8246 (mm) REVERT: I 342 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6506 (tt) REVERT: L 575 GLN cc_start: 0.7272 (tt0) cc_final: 0.6843 (mt0) REVERT: L 610 TRP cc_start: 0.6987 (t-100) cc_final: 0.6601 (t-100) REVERT: L 645 LEU cc_start: 0.8472 (mt) cc_final: 0.7992 (tp) REVERT: L 648 GLU cc_start: 0.7834 (pp20) cc_final: 0.7306 (pp20) REVERT: L 655 LYS cc_start: 0.6702 (mmtt) cc_final: 0.6259 (pttm) outliers start: 65 outliers final: 52 residues processed: 305 average time/residue: 0.1235 time to fit residues: 58.5322 Evaluate side-chains 302 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 365 SER Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 469 ARG Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 519 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 386 ASN Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain L residue 591 GLN Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 628 TRP Chi-restraints excluded: chain L residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN E 137 ASN E 183 GLN I 249 HIS I 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.210472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.178246 restraints weight = 28398.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177612 restraints weight = 25620.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179868 restraints weight = 24777.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.180093 restraints weight = 17491.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180720 restraints weight = 16457.085| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18212 Z= 0.194 Angle : 0.755 19.460 24848 Z= 0.368 Chirality : 0.048 0.256 2945 Planarity : 0.004 0.046 3032 Dihedral : 7.153 48.986 3618 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.59 % Allowed : 15.54 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2099 helix: 1.37 (0.27), residues: 420 sheet: 0.31 (0.19), residues: 679 loop : 0.06 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 100 TYR 0.040 0.002 TYR C 33 PHE 0.023 0.002 PHE E 376 TRP 0.065 0.002 TRP L 596 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00455 (18110) covalent geometry : angle 0.69584 (24579) SS BOND : bond 0.00364 ( 37) SS BOND : angle 1.30517 ( 74) hydrogen bonds : bond 0.04965 ( 693) hydrogen bonds : angle 5.26915 ( 1860) link_ALPHA1-2 : bond 0.00229 ( 3) link_ALPHA1-2 : angle 1.87356 ( 9) link_ALPHA1-3 : bond 0.01584 ( 3) link_ALPHA1-3 : angle 0.69091 ( 9) link_ALPHA1-6 : bond 0.00966 ( 3) link_ALPHA1-6 : angle 1.66768 ( 9) link_BETA1-4 : bond 0.00547 ( 18) link_BETA1-4 : angle 1.89612 ( 54) link_BETA1-6 : bond 0.02647 ( 2) link_BETA1-6 : angle 4.26952 ( 6) link_NAG-ASN : bond 0.00552 ( 36) link_NAG-ASN : angle 4.06719 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4198 Ramachandran restraints generated. 2099 Oldfield, 0 Emsley, 2099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 254 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8792 (mttp) cc_final: 0.8482 (mmtt) REVERT: A 78 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7594 (ttmm) REVERT: A 92 ASP cc_start: 0.8181 (m-30) cc_final: 0.7771 (t0) REVERT: B 88 GLU cc_start: 0.7891 (tp30) cc_final: 0.7661 (tp30) REVERT: C 38 TRP cc_start: 0.7498 (OUTLIER) cc_final: 0.6081 (m-90) REVERT: D 24 LEU cc_start: 0.8605 (mp) cc_final: 0.8289 (mp) REVERT: D 39 ARG cc_start: 0.6268 (mmt-90) cc_final: 0.5946 (mmt-90) REVERT: K 180 ASP cc_start: 0.7658 (m-30) cc_final: 0.7357 (m-30) REVERT: K 199 SER cc_start: 0.9139 (p) cc_final: 0.8538 (m) REVERT: K 234 ASN cc_start: 0.5613 (OUTLIER) cc_final: 0.5128 (p0) REVERT: K 416 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7210 (mt) REVERT: K 475 MET cc_start: 0.8243 (mmm) cc_final: 0.7918 (mmt) REVERT: E 95 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6574 (mtm) REVERT: E 258 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8523 (mm-40) REVERT: E 482 GLU cc_start: 0.6816 (mp0) cc_final: 0.6435 (mp0) REVERT: F 535 MET cc_start: 0.6705 (mmp) cc_final: 0.6468 (mmm) REVERT: I 150 MET cc_start: 0.7578 (mmm) cc_final: 0.7105 (mmt) REVERT: I 213 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8350 (mm) REVERT: I 342 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6499 (tt) REVERT: L 575 GLN cc_start: 0.7230 (tt0) cc_final: 0.6763 (mt0) REVERT: L 648 GLU cc_start: 0.7815 (pp20) cc_final: 0.7527 (pp20) REVERT: L 655 LYS cc_start: 0.6761 (mmtt) cc_final: 0.6387 (pttm) outliers start: 68 outliers final: 55 residues processed: 306 average time/residue: 0.1258 time to fit residues: 59.7194 Evaluate side-chains 301 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 365 SER Chi-restraints excluded: chain K residue 375 SER Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 416 LEU Chi-restraints excluded: chain K residue 469 ARG Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 CYS Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 386 ASN Chi-restraints excluded: chain I residue 392 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 496 VAL Chi-restraints excluded: chain L residue 591 GLN Chi-restraints excluded: chain L residue 599 SER Chi-restraints excluded: chain L residue 628 TRP Chi-restraints excluded: chain L residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 29 optimal weight: 6.9990 chunk 142 optimal weight: 0.0670 chunk 181 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.211990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.177928 restraints weight = 28508.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179670 restraints weight = 24059.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.181272 restraints weight = 19489.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.181701 restraints weight = 13814.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181948 restraints weight = 13297.144| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18212 Z= 0.149 Angle : 0.723 17.877 24848 Z= 0.351 Chirality : 0.046 0.250 2945 Planarity : 0.004 0.045 3032 Dihedral : 6.971 47.610 3618 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.28 % Allowed : 16.38 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2099 helix: 1.29 (0.27), residues: 429 sheet: 0.35 (0.19), residues: 679 loop : 0.10 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.039 0.002 TYR C 33 PHE 0.026 0.002 PHE E 320 TRP 0.064 0.002 TRP L 596 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00339 (18110) covalent geometry : angle 0.66556 (24579) SS BOND : bond 0.00269 ( 37) SS BOND : angle 1.41839 ( 74) hydrogen bonds : bond 0.04604 ( 693) hydrogen bonds : angle 5.17359 ( 1860) link_ALPHA1-2 : bond 0.00212 ( 3) link_ALPHA1-2 : angle 1.91442 ( 9) link_ALPHA1-3 : bond 0.01504 ( 3) link_ALPHA1-3 : angle 0.72770 ( 9) link_ALPHA1-6 : bond 0.00965 ( 3) link_ALPHA1-6 : angle 1.65106 ( 9) link_BETA1-4 : bond 0.00551 ( 18) link_BETA1-4 : angle 1.77271 ( 54) link_BETA1-6 : bond 0.02875 ( 2) link_BETA1-6 : angle 4.39774 ( 6) link_NAG-ASN : bond 0.00529 ( 36) link_NAG-ASN : angle 3.87390 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2775.57 seconds wall clock time: 49 minutes 23.66 seconds (2963.66 seconds total)