Starting phenix.real_space_refine on Wed Mar 4 21:20:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oed_70395/03_2026/9oed_70395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oed_70395/03_2026/9oed_70395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oed_70395/03_2026/9oed_70395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oed_70395/03_2026/9oed_70395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oed_70395/03_2026/9oed_70395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oed_70395/03_2026/9oed_70395.map" } resolution = 3.94 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= 0.018 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 107 5.16 5 C 10080 2.51 5 N 2689 2.21 5 O 3178 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: 16054 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 991 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "K" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} 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: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 5 Chain: "D" 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: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} 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: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, '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: "I" 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: "L" 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: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" 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: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "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: "Y" 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: "Z" 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: 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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 Time building chain proxies: 3.60, per 1000 atoms: 0.22 Number of scatterers: 16054 At special positions: 0 Unit cell: (122.55, 126.35, 167.2, 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 107 16.00 O 3178 8.00 N 2689 7.00 C 10080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.11 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.29 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.05 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS J 605 " distance=2.06 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.14 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 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=2.09 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=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.08 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=2.03 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 P 4 " - " MAN P 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG H 1 " - " FUC H 6 " NAG-ASN " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " 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 339 " " NAG E 606 " - " ASN E 355 " " NAG E 607 " - " ASN E 392 " " NAG G 1 " - " ASN K 234 " " NAG H 1 " - " ASN K 262 " " NAG I 1 " - " ASN K 448 " " 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 339 " " NAG K 606 " - " ASN K 355 " " NAG K 607 " - " ASN K 392 " " NAG L 1 " - " ASN K 295 " " NAG M 1 " - " ASN K 301 " " NAG N 1 " - " ASN K 332 " " NAG O 1 " - " ASN K 386 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 448 " " NAG R 1 " - " ASN C 295 " " NAG S 1 " - " ASN C 332 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN E 262 " " NAG V 1 " - " ASN E 448 " " NAG W 1 " - " ASN E 295 " " NAG X 1 " - " ASN E 301 " " NAG Y 1 " - " ASN E 332 " " NAG Z 1 " - " ASN E 386 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 814.3 milliseconds 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 28 sheets defined 26.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'K' and resid 70 through 74 Processing helix chain 'K' and resid 98 through 117 removed outlier: 4.251A pdb=" N GLU K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.668A pdb=" N LYS K 351 " --> pdb=" O LYS K 347 " (cutoff:3.500A) removed outlier: 3.998A 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 425 through 429 removed outlier: 4.143A pdb=" N GLN K 428 " --> pdb=" O ASN K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 484 removed outlier: 3.793A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU K 482 " --> pdb=" O ASN K 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.237A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 removed outlier: 3.625A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 Processing helix chain 'J' and resid 570 through 596 Processing helix chain 'J' and resid 611 through 615 removed outlier: 3.516A pdb=" N SER J 615 " --> pdb=" O SER J 612 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 626 removed outlier: 3.673A pdb=" N MET J 626 " --> pdb=" O ILE J 622 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 3.714A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.650A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.268A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.838A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.856A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.544A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.599A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.983A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.570A pdb=" N LYS D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.697A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.676A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.604A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.146A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.507A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.725A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.029A 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 425 through 429 removed outlier: 3.664A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.694A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.502A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 597 Processing helix chain 'F' and resid 611 through 615 removed outlier: 3.539A pdb=" N SER F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.696A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.728A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.618A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 11 through 12 current: chain 'A' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 60 through 61 current: chain 'A' and resid 117 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 7.601A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.395A pdb=" N VAL J 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VAL K 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR J 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N TYR K 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N CYS J 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.534A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'K' and resid 201 through 203 removed outlier: 6.385A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 260 current: chain 'K' and resid 284 through 298 removed outlier: 6.954A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR K 297 " --> pdb=" O HIS K 330 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 329 through 334 current: chain 'K' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 381 through 385 current: chain 'K' and resid 465 through 470 Processing sheet with id=AB4, first strand: chain 'K' and resid 301 through 307 removed outlier: 7.038A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.478A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.452A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.480A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 260 current: chain 'C' and resid 284 through 307 removed outlier: 4.115A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS C 305 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 317 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC3, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.484A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.370A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 260 current: chain 'E' and resid 284 through 298 removed outlier: 7.044A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AD1, first strand: chain 'E' and resid 301 through 307 removed outlier: 4.174A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS E 305 " --> pdb=" O PHE E 320 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1335 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: 2.47 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4518 1.33 - 1.46: 4232 1.46 - 1.59: 7478 1.59 - 1.72: 0 1.72 - 1.85: 144 Bond restraints: 16372 Sorted by residual: bond pdb=" NE1 TRP A 116 " pdb=" CE2 TRP A 116 " ideal model delta sigma weight residual 1.370 1.331 0.039 1.10e-02 8.26e+03 1.25e+01 bond pdb=" CB HIS B 90 " pdb=" CG HIS B 90 " ideal model delta sigma weight residual 1.497 1.455 0.042 1.40e-02 5.10e+03 8.91e+00 bond pdb=" NE ARG C 350 " pdb=" CZ ARG C 350 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 6.86e+00 bond pdb=" NE ARG C 166 " pdb=" CZ ARG C 166 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.10e-02 8.26e+03 6.68e+00 bond pdb=" NE ARG B 61 " pdb=" CZ ARG B 61 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.10e-02 8.26e+03 6.45e+00 ... (remaining 16367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 20486 2.08 - 4.17: 1440 4.17 - 6.25: 252 6.25 - 8.33: 44 8.33 - 10.42: 1 Bond angle restraints: 22223 Sorted by residual: angle pdb=" C THR A 111 " pdb=" N PRO A 112 " pdb=" CA PRO A 112 " ideal model delta sigma weight residual 119.56 127.80 -8.24 1.02e+00 9.61e-01 6.52e+01 angle pdb=" C ALA K 436 " pdb=" N PRO K 437 " pdb=" CA PRO K 437 " ideal model delta sigma weight residual 119.66 125.19 -5.53 7.20e-01 1.93e+00 5.89e+01 angle pdb=" C GLN A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.66 125.16 -5.50 7.30e-01 1.88e+00 5.67e+01 angle pdb=" C CYS K 239 " pdb=" N PRO K 240 " pdb=" CA PRO K 240 " ideal model delta sigma weight residual 119.56 127.22 -7.66 1.02e+00 9.61e-01 5.64e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 125.02 -5.36 7.20e-01 1.93e+00 5.55e+01 ... (remaining 22218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 10383 21.25 - 42.49: 226 42.49 - 63.74: 67 63.74 - 84.98: 29 84.98 - 106.23: 15 Dihedral angle restraints: 10720 sinusoidal: 5181 harmonic: 5539 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 97 " pdb=" CB CYS A 97 " ideal model delta sinusoidal sigma weight residual 93.00 48.22 44.78 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.35 43.35 1 1.00e+01 1.00e-02 2.62e+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 -127.99 41.99 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 10717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 2691 0.366 - 0.731: 9 0.731 - 1.097: 1 1.097 - 1.462: 2 1.462 - 1.828: 3 Chirality restraints: 2706 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 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.23e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.94e+02 ... (remaining 2703 not shown) Planarity restraints: 2768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 386 " -0.065 2.00e-02 2.50e+03 6.49e-02 5.27e+01 pdb=" CG ASN K 386 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN K 386 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN K 386 " 0.098 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " -0.056 2.00e-02 2.50e+03 5.70e-02 4.07e+01 pdb=" CG ASN C 339 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " 0.088 2.00e-02 2.50e+03 pdb=" C1 NAG C 607 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 262 " 0.050 2.00e-02 2.50e+03 5.33e-02 3.55e+01 pdb=" CG ASN C 262 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 262 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 262 " -0.084 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.064 2.00e-02 2.50e+03 ... (remaining 2765 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 56 2.60 - 3.17: 13470 3.17 - 3.75: 22077 3.75 - 4.32: 33015 4.32 - 4.90: 52737 Nonbonded interactions: 121355 Sorted by model distance: nonbonded pdb=" O3 NAG H 2 " pdb=" O7 NAG H 2 " model vdw 2.020 3.040 nonbonded pdb=" C3 NAG H 2 " pdb=" O7 NAG H 2 " model vdw 2.278 3.470 nonbonded pdb=" O5 NAG G 1 " pdb=" O6 NAG G 1 " model vdw 2.331 2.432 nonbonded pdb=" N ASN E 355 " pdb=" OD1 ASN E 355 " model vdw 2.404 3.120 nonbonded pdb=" OG1 THR K 37 " pdb=" OG1 THR K 499 " model vdw 2.439 3.040 ... (remaining 121350 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 'C' and resid 31 through 607) selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) } ncs_group { reference = chain 'P' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.012 0.255 16476 Z= 0.632 Angle : 1.366 18.522 22500 Z= 0.826 Chirality : 0.102 1.828 2706 Planarity : 0.005 0.051 2727 Dihedral : 11.286 106.228 7031 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.35 % Allowed : 0.24 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 2.39 (0.19), residues: 1868 helix: 0.05 (0.21), residues: 420 sheet: 1.54 (0.20), residues: 542 loop : 2.75 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.040 0.004 TYR E 40 PHE 0.015 0.003 PHE B 98 TRP 0.030 0.005 TRP K 479 HIS 0.005 0.001 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.01087 (16372) covalent geometry : angle 1.22679 (22223) SS BOND : bond 0.05117 ( 35) SS BOND : angle 3.53545 ( 70) hydrogen bonds : bond 0.24634 ( 511) hydrogen bonds : angle 7.06896 ( 1335) link_ALPHA1-2 : bond 0.04504 ( 3) link_ALPHA1-2 : angle 7.48917 ( 9) link_ALPHA1-3 : bond 0.04646 ( 3) link_ALPHA1-3 : angle 4.01939 ( 9) link_BETA1-4 : bond 0.04289 ( 20) link_BETA1-4 : angle 7.15657 ( 60) link_BETA1-6 : bond 0.02357 ( 2) link_BETA1-6 : angle 5.05999 ( 6) link_NAG-ASN : bond 0.06867 ( 41) link_NAG-ASN : angle 5.55295 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 466 time to evaluate : 0.575 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 33 TYR cc_start: 0.8674 (m-80) cc_final: 0.7911 (m-10) REVERT: A 67 ASN cc_start: 0.8076 (m-40) cc_final: 0.7656 (p0) REVERT: A 99 ARG cc_start: 0.8311 (ttp-170) cc_final: 0.7845 (ttp-170) REVERT: B 17 ASP cc_start: 0.7160 (m-30) cc_final: 0.6930 (t0) REVERT: B 47 LEU cc_start: 0.8470 (mt) cc_final: 0.8043 (mt) REVERT: K 82 GLN cc_start: 0.8203 (mt0) cc_final: 0.7994 (mp10) REVERT: K 346 VAL cc_start: 0.8169 (t) cc_final: 0.7911 (p) REVERT: K 355 ASN cc_start: 0.5113 (OUTLIER) cc_final: 0.4517 (t0) REVERT: K 377 ASN cc_start: 0.8659 (t0) cc_final: 0.8112 (p0) REVERT: K 481 SER cc_start: 0.8622 (p) cc_final: 0.8108 (t) REVERT: J 535 MET cc_start: 0.8029 (mmp) cc_final: 0.7743 (mtm) REVERT: J 631 TRP cc_start: 0.8185 (t-100) cc_final: 0.7746 (t-100) REVERT: J 638 TYR cc_start: 0.8062 (m-80) cc_final: 0.7761 (m-10) REVERT: J 647 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 53 PHE cc_start: 0.7264 (p90) cc_final: 0.7042 (p90) REVERT: C 97 LYS cc_start: 0.8622 (mttt) cc_final: 0.8111 (tmmt) REVERT: C 232 LYS cc_start: 0.7643 (mttt) cc_final: 0.6836 (tttp) REVERT: C 478 ASN cc_start: 0.8297 (m-40) cc_final: 0.7913 (t0) REVERT: D 655 LYS cc_start: 0.8701 (tptp) cc_final: 0.8441 (pttt) REVERT: E 104 MET cc_start: 0.9058 (ttm) cc_final: 0.8806 (tpp) REVERT: E 161 MET cc_start: 0.8283 (tpp) cc_final: 0.7910 (tpt) REVERT: E 180 ASP cc_start: 0.8462 (m-30) cc_final: 0.8246 (m-30) REVERT: E 390 LEU cc_start: 0.8704 (mt) cc_final: 0.8311 (mt) REVERT: E 423 ILE cc_start: 0.8965 (mt) cc_final: 0.8210 (mt) outliers start: 6 outliers final: 1 residues processed: 471 average time/residue: 0.1293 time to fit residues: 90.2559 Evaluate side-chains 246 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 355 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN K 246 GLN ** K 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN D 651 ASN E 103 GLN E 114 GLN E 195 ASN F 585 HIS F 653 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131748 restraints weight = 25810.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133701 restraints weight = 20005.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135075 restraints weight = 15706.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135941 restraints weight = 13478.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136234 restraints weight = 12352.888| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16476 Z= 0.170 Angle : 0.761 13.189 22500 Z= 0.370 Chirality : 0.050 0.371 2706 Planarity : 0.004 0.044 2727 Dihedral : 8.291 71.488 3462 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 3.12 % Allowed : 9.13 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 2.00 (0.19), residues: 1868 helix: 1.77 (0.27), residues: 408 sheet: 1.22 (0.21), residues: 542 loop : 1.41 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 39 TYR 0.023 0.002 TYR K 484 PHE 0.019 0.002 PHE B 98 TRP 0.018 0.002 TRP F 623 HIS 0.010 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00360 (16372) covalent geometry : angle 0.70006 (22223) SS BOND : bond 0.00364 ( 35) SS BOND : angle 1.29387 ( 70) hydrogen bonds : bond 0.07567 ( 511) hydrogen bonds : angle 5.51824 ( 1335) link_ALPHA1-2 : bond 0.00697 ( 3) link_ALPHA1-2 : angle 2.93493 ( 9) link_ALPHA1-3 : bond 0.01216 ( 3) link_ALPHA1-3 : angle 1.68960 ( 9) link_BETA1-4 : bond 0.00641 ( 20) link_BETA1-4 : angle 2.62921 ( 60) link_BETA1-6 : bond 0.01682 ( 2) link_BETA1-6 : angle 3.08719 ( 6) link_NAG-ASN : bond 0.00714 ( 41) link_NAG-ASN : angle 3.44078 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TYR cc_start: 0.8711 (m-80) cc_final: 0.8392 (m-80) REVERT: B 79 GLN cc_start: 0.7959 (mp10) cc_final: 0.7603 (mp10) REVERT: B 82 ASP cc_start: 0.8585 (m-30) cc_final: 0.8237 (m-30) REVERT: B 91 SER cc_start: 0.8547 (t) cc_final: 0.8244 (p) REVERT: K 82 GLN cc_start: 0.8073 (mt0) cc_final: 0.7831 (mp10) REVERT: K 346 VAL cc_start: 0.7890 (t) cc_final: 0.7559 (m) REVERT: K 377 ASN cc_start: 0.8693 (t0) cc_final: 0.8111 (p0) REVERT: J 535 MET cc_start: 0.7885 (mmp) cc_final: 0.7515 (mpp) REVERT: J 631 TRP cc_start: 0.8449 (t-100) cc_final: 0.7906 (t-100) REVERT: J 647 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 97 LYS cc_start: 0.8429 (mttt) cc_final: 0.8000 (tmmt) REVERT: C 180 ASP cc_start: 0.8290 (m-30) cc_final: 0.8078 (t0) REVERT: C 303 THR cc_start: 0.8816 (m) cc_final: 0.8577 (p) REVERT: D 543 ASN cc_start: 0.7477 (t0) cc_final: 0.7170 (t0) REVERT: D 590 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7204 (tm-30) REVERT: D 639 THR cc_start: 0.8526 (p) cc_final: 0.8297 (t) REVERT: D 648 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: D 655 LYS cc_start: 0.8581 (tptp) cc_final: 0.8125 (pttp) REVERT: D 658 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7696 (pp30) REVERT: E 50 THR cc_start: 0.9101 (t) cc_final: 0.8866 (m) outliers start: 53 outliers final: 38 residues processed: 320 average time/residue: 0.1209 time to fit residues: 58.9617 Evaluate side-chains 264 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 0.0060 chunk 186 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 37 GLN K 398 ASN J 630 GLN C 258 GLN C 425 ASN E 170 GLN F 585 HIS F 653 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130862 restraints weight = 25880.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132668 restraints weight = 22050.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134049 restraints weight = 18035.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134614 restraints weight = 14831.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134873 restraints weight = 13751.177| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16476 Z= 0.136 Angle : 0.673 13.563 22500 Z= 0.324 Chirality : 0.048 0.282 2706 Planarity : 0.004 0.049 2727 Dihedral : 7.349 57.872 3459 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.36 % Allowed : 10.49 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 1.64 (0.19), residues: 1868 helix: 2.00 (0.28), residues: 414 sheet: 0.96 (0.21), residues: 579 loop : 0.90 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 500 TYR 0.022 0.001 TYR J 638 PHE 0.018 0.002 PHE C 53 TRP 0.010 0.001 TRP E 479 HIS 0.008 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00291 (16372) covalent geometry : angle 0.61429 (22223) SS BOND : bond 0.00264 ( 35) SS BOND : angle 0.92368 ( 70) hydrogen bonds : bond 0.05976 ( 511) hydrogen bonds : angle 5.01699 ( 1335) link_ALPHA1-2 : bond 0.00381 ( 3) link_ALPHA1-2 : angle 2.49527 ( 9) link_ALPHA1-3 : bond 0.01152 ( 3) link_ALPHA1-3 : angle 1.24100 ( 9) link_BETA1-4 : bond 0.00534 ( 20) link_BETA1-4 : angle 2.45006 ( 60) link_BETA1-6 : bond 0.01791 ( 2) link_BETA1-6 : angle 3.66476 ( 6) link_NAG-ASN : bond 0.00660 ( 41) link_NAG-ASN : angle 3.14913 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TYR cc_start: 0.8733 (m-80) cc_final: 0.8477 (m-80) REVERT: A 53 TYR cc_start: 0.8130 (m-80) cc_final: 0.7911 (m-80) REVERT: B 42 GLU cc_start: 0.7671 (pm20) cc_final: 0.7389 (pm20) REVERT: B 82 ASP cc_start: 0.8618 (m-30) cc_final: 0.8347 (m-30) REVERT: B 91 SER cc_start: 0.8541 (t) cc_final: 0.8222 (p) REVERT: B 102 THR cc_start: 0.8699 (m) cc_final: 0.8490 (m) REVERT: K 82 GLN cc_start: 0.8038 (mt0) cc_final: 0.7833 (mp10) REVERT: K 91 GLU cc_start: 0.7207 (tp30) cc_final: 0.6894 (tp30) REVERT: K 377 ASN cc_start: 0.8628 (t0) cc_final: 0.8138 (p0) REVERT: K 434 MET cc_start: 0.8357 (tmm) cc_final: 0.8034 (ttt) REVERT: J 535 MET cc_start: 0.7899 (mmp) cc_final: 0.7455 (mpp) REVERT: J 631 TRP cc_start: 0.8418 (t-100) cc_final: 0.7914 (t-100) REVERT: C 97 LYS cc_start: 0.8386 (mttt) cc_final: 0.8167 (tmmt) REVERT: C 303 THR cc_start: 0.8766 (m) cc_final: 0.8563 (p) REVERT: D 543 ASN cc_start: 0.7612 (t0) cc_final: 0.7362 (t0) REVERT: D 590 GLN cc_start: 0.7549 (mm-40) cc_final: 0.6822 (tm-30) REVERT: D 648 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7865 (pt0) REVERT: D 655 LYS cc_start: 0.8413 (tptp) cc_final: 0.8196 (pttm) REVERT: E 50 THR cc_start: 0.9093 (t) cc_final: 0.8874 (m) REVERT: E 180 ASP cc_start: 0.8740 (m-30) cc_final: 0.7952 (m-30) REVERT: E 423 ILE cc_start: 0.8814 (mt) cc_final: 0.8236 (mt) outliers start: 57 outliers final: 44 residues processed: 282 average time/residue: 0.1156 time to fit residues: 49.5497 Evaluate side-chains 268 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 6 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN J 630 GLN F 585 HIS F 618 ASN F 653 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128837 restraints weight = 25856.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130121 restraints weight = 21266.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131071 restraints weight = 18026.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131497 restraints weight = 16145.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131769 restraints weight = 15080.200| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16476 Z= 0.131 Angle : 0.643 12.766 22500 Z= 0.308 Chirality : 0.047 0.269 2706 Planarity : 0.004 0.053 2727 Dihedral : 6.695 59.126 3459 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.12 % Allowed : 10.72 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 1.37 (0.19), residues: 1868 helix: 2.05 (0.27), residues: 414 sheet: 0.79 (0.21), residues: 579 loop : 0.57 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 500 TYR 0.026 0.001 TYR J 638 PHE 0.014 0.002 PHE F 522 TRP 0.020 0.001 TRP F 610 HIS 0.009 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00281 (16372) covalent geometry : angle 0.59235 (22223) SS BOND : bond 0.00566 ( 35) SS BOND : angle 0.98444 ( 70) hydrogen bonds : bond 0.05121 ( 511) hydrogen bonds : angle 4.79079 ( 1335) link_ALPHA1-2 : bond 0.00296 ( 3) link_ALPHA1-2 : angle 2.19083 ( 9) link_ALPHA1-3 : bond 0.01177 ( 3) link_ALPHA1-3 : angle 1.22554 ( 9) link_BETA1-4 : bond 0.00529 ( 20) link_BETA1-4 : angle 2.18259 ( 60) link_BETA1-6 : bond 0.02120 ( 2) link_BETA1-6 : angle 3.44775 ( 6) link_NAG-ASN : bond 0.00609 ( 41) link_NAG-ASN : angle 2.88488 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.8161 (m-80) cc_final: 0.7921 (m-80) REVERT: B 42 GLU cc_start: 0.7588 (pm20) cc_final: 0.7334 (pm20) REVERT: B 82 ASP cc_start: 0.8649 (m-30) cc_final: 0.8330 (m-30) REVERT: B 91 SER cc_start: 0.8389 (t) cc_final: 0.8099 (p) REVERT: K 82 GLN cc_start: 0.8138 (mt0) cc_final: 0.7825 (mp10) REVERT: K 377 ASN cc_start: 0.8646 (t0) cc_final: 0.8130 (p0) REVERT: K 434 MET cc_start: 0.8368 (tmm) cc_final: 0.8042 (ttt) REVERT: K 475 MET cc_start: 0.7848 (mmm) cc_final: 0.7605 (mmt) REVERT: J 535 MET cc_start: 0.8006 (mmp) cc_final: 0.7526 (mpp) REVERT: J 631 TRP cc_start: 0.8476 (t-100) cc_final: 0.7873 (t-100) REVERT: J 654 GLU cc_start: 0.7921 (tp30) cc_final: 0.7600 (tp30) REVERT: C 97 LYS cc_start: 0.8455 (mttt) cc_final: 0.7986 (tmmt) REVERT: D 543 ASN cc_start: 0.7610 (t0) cc_final: 0.7409 (t0) REVERT: D 590 GLN cc_start: 0.7605 (mm-40) cc_final: 0.6987 (tm-30) REVERT: D 648 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7931 (pt0) REVERT: D 655 LYS cc_start: 0.8551 (tptp) cc_final: 0.8340 (pttm) REVERT: D 658 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7606 (pp30) REVERT: E 50 THR cc_start: 0.9105 (t) cc_final: 0.8878 (m) REVERT: E 180 ASP cc_start: 0.8672 (m-30) cc_final: 0.7831 (m-30) REVERT: E 423 ILE cc_start: 0.8790 (mt) cc_final: 0.8079 (mt) outliers start: 70 outliers final: 49 residues processed: 282 average time/residue: 0.1088 time to fit residues: 47.3507 Evaluate side-chains 265 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain K residue 491 ILE Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 6 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN K 216 HIS ** J 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 216 HIS F 585 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116832 restraints weight = 26066.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117759 restraints weight = 23652.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119332 restraints weight = 19551.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119748 restraints weight = 16527.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120022 restraints weight = 15527.369| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16476 Z= 0.200 Angle : 0.701 12.378 22500 Z= 0.342 Chirality : 0.049 0.309 2706 Planarity : 0.004 0.053 2727 Dihedral : 6.670 55.097 3459 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.18 % Allowed : 11.55 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.19), residues: 1868 helix: 1.53 (0.27), residues: 432 sheet: 0.64 (0.21), residues: 535 loop : 0.16 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 503 TYR 0.021 0.002 TYR J 638 PHE 0.018 0.002 PHE E 383 TRP 0.016 0.002 TRP F 610 HIS 0.009 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00469 (16372) covalent geometry : angle 0.65244 (22223) SS BOND : bond 0.00525 ( 35) SS BOND : angle 1.42102 ( 70) hydrogen bonds : bond 0.05538 ( 511) hydrogen bonds : angle 4.92868 ( 1335) link_ALPHA1-2 : bond 0.00271 ( 3) link_ALPHA1-2 : angle 2.11098 ( 9) link_ALPHA1-3 : bond 0.01267 ( 3) link_ALPHA1-3 : angle 1.32447 ( 9) link_BETA1-4 : bond 0.00463 ( 20) link_BETA1-4 : angle 2.19121 ( 60) link_BETA1-6 : bond 0.01911 ( 2) link_BETA1-6 : angle 3.35151 ( 6) link_NAG-ASN : bond 0.00727 ( 41) link_NAG-ASN : angle 2.91927 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 226 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TYR cc_start: 0.8587 (m-80) cc_final: 0.8305 (m-10) REVERT: B 42 GLU cc_start: 0.7655 (pm20) cc_final: 0.7407 (pm20) REVERT: B 91 SER cc_start: 0.8396 (t) cc_final: 0.8099 (p) REVERT: K 82 GLN cc_start: 0.8183 (mt0) cc_final: 0.7829 (mp10) REVERT: K 377 ASN cc_start: 0.8760 (t0) cc_final: 0.8193 (p0) REVERT: K 434 MET cc_start: 0.8354 (tmm) cc_final: 0.8021 (ttt) REVERT: J 535 MET cc_start: 0.8025 (mmp) cc_final: 0.7607 (mpp) REVERT: J 617 ARG cc_start: 0.8444 (mtt90) cc_final: 0.8162 (mtt90) REVERT: J 631 TRP cc_start: 0.8510 (t-100) cc_final: 0.7924 (t-100) REVERT: J 647 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: J 654 GLU cc_start: 0.8001 (tp30) cc_final: 0.7663 (tp30) REVERT: C 92 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6485 (mm-30) REVERT: C 97 LYS cc_start: 0.8499 (mttt) cc_final: 0.7995 (tmmt) REVERT: D 543 ASN cc_start: 0.7653 (t0) cc_final: 0.7391 (t0) REVERT: D 590 GLN cc_start: 0.7578 (mm-40) cc_final: 0.6990 (tm-30) REVERT: D 648 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: D 655 LYS cc_start: 0.8578 (tptp) cc_final: 0.8288 (pttm) outliers start: 71 outliers final: 58 residues processed: 273 average time/residue: 0.1179 time to fit residues: 49.3878 Evaluate side-chains 263 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 131 CYS Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 621 GLU Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN J 630 GLN F 585 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113002 restraints weight = 26241.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114984 restraints weight = 20590.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115584 restraints weight = 18317.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116203 restraints weight = 15538.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116753 restraints weight = 14136.662| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16476 Z= 0.215 Angle : 0.745 11.584 22500 Z= 0.363 Chirality : 0.049 0.280 2706 Planarity : 0.004 0.052 2727 Dihedral : 6.880 54.823 3459 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.07 % Allowed : 12.26 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.44 (0.19), residues: 1868 helix: 1.26 (0.27), residues: 435 sheet: 0.38 (0.22), residues: 496 loop : -0.14 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 503 TYR 0.024 0.002 TYR J 638 PHE 0.023 0.002 PHE E 383 TRP 0.023 0.002 TRP A 116 HIS 0.012 0.002 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00504 (16372) covalent geometry : angle 0.69999 (22223) SS BOND : bond 0.00414 ( 35) SS BOND : angle 1.34566 ( 70) hydrogen bonds : bond 0.05730 ( 511) hydrogen bonds : angle 5.02146 ( 1335) link_ALPHA1-2 : bond 0.00246 ( 3) link_ALPHA1-2 : angle 2.08985 ( 9) link_ALPHA1-3 : bond 0.01221 ( 3) link_ALPHA1-3 : angle 1.31009 ( 9) link_BETA1-4 : bond 0.00449 ( 20) link_BETA1-4 : angle 2.15688 ( 60) link_BETA1-6 : bond 0.02015 ( 2) link_BETA1-6 : angle 3.40407 ( 6) link_NAG-ASN : bond 0.00750 ( 41) link_NAG-ASN : angle 2.93584 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 228 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TYR cc_start: 0.8760 (m-80) cc_final: 0.8419 (m-10) REVERT: A 101 PHE cc_start: 0.8567 (t80) cc_final: 0.8295 (t80) REVERT: A 116 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7121 (p-90) REVERT: B 42 GLU cc_start: 0.7714 (pm20) cc_final: 0.7501 (pm20) REVERT: B 79 GLN cc_start: 0.8151 (mp10) cc_final: 0.7852 (mp10) REVERT: K 82 GLN cc_start: 0.8147 (mt0) cc_final: 0.7819 (mp10) REVERT: K 115 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8804 (t) REVERT: K 377 ASN cc_start: 0.8783 (t0) cc_final: 0.8140 (p0) REVERT: K 381 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: J 535 MET cc_start: 0.8020 (mmp) cc_final: 0.7619 (mpp) REVERT: J 631 TRP cc_start: 0.8498 (t-100) cc_final: 0.7982 (t-100) REVERT: C 151 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.7017 (ptp-170) REVERT: C 153 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6522 (tp30) REVERT: C 180 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8107 (t70) REVERT: C 482 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: D 648 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: D 658 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7341 (pp30) REVERT: E 180 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8611 (t0) outliers start: 86 outliers final: 62 residues processed: 281 average time/residue: 0.1151 time to fit residues: 49.5154 Evaluate side-chains 271 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 131 CYS Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 621 GLU Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 148 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN C 258 GLN E 195 ASN F 585 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116023 restraints weight = 26030.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117642 restraints weight = 20053.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118626 restraints weight = 16867.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119141 restraints weight = 14651.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119516 restraints weight = 13577.878| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16476 Z= 0.134 Angle : 0.650 11.442 22500 Z= 0.316 Chirality : 0.046 0.282 2706 Planarity : 0.004 0.057 2727 Dihedral : 6.436 51.386 3459 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.65 % Allowed : 13.91 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.52 (0.19), residues: 1868 helix: 1.46 (0.27), residues: 432 sheet: 0.35 (0.22), residues: 531 loop : -0.11 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 503 TYR 0.018 0.001 TYR J 638 PHE 0.011 0.002 PHE E 383 TRP 0.041 0.001 TRP F 610 HIS 0.011 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00301 (16372) covalent geometry : angle 0.60270 (22223) SS BOND : bond 0.00225 ( 35) SS BOND : angle 1.32925 ( 70) hydrogen bonds : bond 0.04856 ( 511) hydrogen bonds : angle 4.80162 ( 1335) link_ALPHA1-2 : bond 0.00256 ( 3) link_ALPHA1-2 : angle 2.06356 ( 9) link_ALPHA1-3 : bond 0.01240 ( 3) link_ALPHA1-3 : angle 1.33382 ( 9) link_BETA1-4 : bond 0.00433 ( 20) link_BETA1-4 : angle 1.90174 ( 60) link_BETA1-6 : bond 0.01971 ( 2) link_BETA1-6 : angle 3.35694 ( 6) link_NAG-ASN : bond 0.00613 ( 41) link_NAG-ASN : angle 2.80376 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 220 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TYR cc_start: 0.8648 (m-80) cc_final: 0.8434 (m-10) REVERT: A 101 PHE cc_start: 0.8481 (t80) cc_final: 0.8277 (t80) REVERT: B 79 GLN cc_start: 0.8213 (mp10) cc_final: 0.7849 (mp10) REVERT: K 82 GLN cc_start: 0.8153 (mt0) cc_final: 0.7823 (mp10) REVERT: K 115 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8813 (t) REVERT: K 377 ASN cc_start: 0.8790 (t0) cc_final: 0.8133 (p0) REVERT: K 381 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: J 631 TRP cc_start: 0.8494 (t-100) cc_final: 0.7890 (t-100) REVERT: C 97 LYS cc_start: 0.8720 (mptt) cc_final: 0.8495 (mmtm) REVERT: C 151 ARG cc_start: 0.7204 (ptp-170) cc_final: 0.6967 (ptp-170) REVERT: C 153 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6306 (tp30) REVERT: C 180 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8068 (t70) REVERT: C 482 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: D 589 ASP cc_start: 0.8476 (t70) cc_final: 0.8210 (t0) REVERT: D 658 GLN cc_start: 0.7771 (tm-30) cc_final: 0.6959 (pt0) REVERT: F 610 TRP cc_start: 0.5920 (t-100) cc_final: 0.5719 (t60) outliers start: 62 outliers final: 43 residues processed: 258 average time/residue: 0.1135 time to fit residues: 45.6311 Evaluate side-chains 256 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 131 CYS Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 621 GLU Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN C 258 GLN F 570 HIS F 585 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109433 restraints weight = 26821.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110628 restraints weight = 24804.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111842 restraints weight = 19297.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112458 restraints weight = 16223.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112636 restraints weight = 15507.884| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16476 Z= 0.264 Angle : 0.788 11.559 22500 Z= 0.387 Chirality : 0.050 0.293 2706 Planarity : 0.005 0.055 2727 Dihedral : 7.228 59.696 3459 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.36 % Allowed : 13.49 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.03 (0.19), residues: 1868 helix: 1.08 (0.26), residues: 432 sheet: -0.10 (0.22), residues: 540 loop : -0.31 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 503 TYR 0.021 0.002 TYR J 638 PHE 0.022 0.003 PHE E 383 TRP 0.030 0.002 TRP F 610 HIS 0.011 0.002 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00626 (16372) covalent geometry : angle 0.74243 (22223) SS BOND : bond 0.00500 ( 35) SS BOND : angle 1.51514 ( 70) hydrogen bonds : bond 0.06129 ( 511) hydrogen bonds : angle 5.12914 ( 1335) link_ALPHA1-2 : bond 0.00250 ( 3) link_ALPHA1-2 : angle 2.05838 ( 9) link_ALPHA1-3 : bond 0.01289 ( 3) link_ALPHA1-3 : angle 1.38756 ( 9) link_BETA1-4 : bond 0.00409 ( 20) link_BETA1-4 : angle 2.12926 ( 60) link_BETA1-6 : bond 0.01732 ( 2) link_BETA1-6 : angle 3.24352 ( 6) link_NAG-ASN : bond 0.00741 ( 41) link_NAG-ASN : angle 3.07453 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 213 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TYR cc_start: 0.8844 (m-80) cc_final: 0.8586 (m-10) REVERT: A 101 PHE cc_start: 0.8608 (t80) cc_final: 0.8390 (t80) REVERT: A 116 TRP cc_start: 0.7978 (p-90) cc_final: 0.7443 (p-90) REVERT: K 82 GLN cc_start: 0.8203 (mt0) cc_final: 0.7834 (mp10) REVERT: K 87 GLU cc_start: 0.7786 (tt0) cc_final: 0.7575 (tt0) REVERT: K 115 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8867 (t) REVERT: K 381 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: J 631 TRP cc_start: 0.8504 (t-100) cc_final: 0.7951 (t-100) REVERT: C 97 LYS cc_start: 0.8751 (mptt) cc_final: 0.8511 (mmtm) REVERT: C 151 ARG cc_start: 0.7376 (ptp-170) cc_final: 0.7134 (ptp-170) REVERT: C 153 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6650 (tp30) REVERT: C 180 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8154 (t70) REVERT: C 482 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: D 589 ASP cc_start: 0.8437 (t70) cc_final: 0.8148 (t0) REVERT: D 648 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: E 207 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7630 (mttp) outliers start: 74 outliers final: 53 residues processed: 261 average time/residue: 0.1151 time to fit residues: 47.3697 Evaluate side-chains 257 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 131 CYS Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 345 VAL Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 381 GLU Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 621 GLU Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 69 optimal weight: 1.9990 chunk 167 optimal weight: 0.2980 chunk 179 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 650 GLN F 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113782 restraints weight = 26138.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115855 restraints weight = 22170.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116967 restraints weight = 17925.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117438 restraints weight = 14592.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117885 restraints weight = 13530.291| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16476 Z= 0.137 Angle : 0.667 11.271 22500 Z= 0.325 Chirality : 0.047 0.273 2706 Planarity : 0.004 0.062 2727 Dihedral : 6.689 56.849 3459 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.18 % Allowed : 14.97 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1868 helix: 1.35 (0.27), residues: 432 sheet: -0.03 (0.22), residues: 528 loop : -0.32 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 503 TYR 0.015 0.001 TYR J 638 PHE 0.013 0.002 PHE B 71 TRP 0.026 0.001 TRP F 610 HIS 0.011 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00310 (16372) covalent geometry : angle 0.62098 (22223) SS BOND : bond 0.00287 ( 35) SS BOND : angle 1.43006 ( 70) hydrogen bonds : bond 0.04977 ( 511) hydrogen bonds : angle 4.79139 ( 1335) link_ALPHA1-2 : bond 0.00217 ( 3) link_ALPHA1-2 : angle 2.03620 ( 9) link_ALPHA1-3 : bond 0.01161 ( 3) link_ALPHA1-3 : angle 1.37651 ( 9) link_BETA1-4 : bond 0.00399 ( 20) link_BETA1-4 : angle 1.86146 ( 60) link_BETA1-6 : bond 0.02006 ( 2) link_BETA1-6 : angle 3.37355 ( 6) link_NAG-ASN : bond 0.00587 ( 41) link_NAG-ASN : angle 2.78612 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 GLN cc_start: 0.8341 (mp10) cc_final: 0.8117 (mp10) REVERT: K 82 GLN cc_start: 0.8103 (mt0) cc_final: 0.7826 (mp10) REVERT: K 115 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8836 (t) REVERT: K 377 ASN cc_start: 0.8743 (t0) cc_final: 0.7982 (p0) REVERT: K 475 MET cc_start: 0.8097 (mmm) cc_final: 0.7750 (mmp) REVERT: J 631 TRP cc_start: 0.8472 (t-100) cc_final: 0.7932 (t-100) REVERT: C 180 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8135 (t70) REVERT: C 482 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: D 589 ASP cc_start: 0.8421 (t70) cc_final: 0.8161 (t0) REVERT: D 648 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: D 658 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7061 (pt0) outliers start: 54 outliers final: 40 residues processed: 254 average time/residue: 0.1133 time to fit residues: 45.1677 Evaluate side-chains 249 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 131 CYS Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 621 GLU Chi-restraints excluded: chain J residue 629 LEU Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 90 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 93 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 630 GLN F 585 HIS F 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122672 restraints weight = 25410.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122427 restraints weight = 28665.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123130 restraints weight = 27310.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123571 restraints weight = 22455.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123811 restraints weight = 20463.225| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16476 Z= 0.140 Angle : 0.658 11.241 22500 Z= 0.320 Chirality : 0.046 0.279 2706 Planarity : 0.004 0.060 2727 Dihedral : 6.470 54.350 3459 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.53 % Allowed : 15.38 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.20 (0.19), residues: 1868 helix: 1.42 (0.27), residues: 432 sheet: -0.00 (0.22), residues: 528 loop : -0.33 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 503 TYR 0.015 0.001 TYR J 638 PHE 0.015 0.002 PHE B 71 TRP 0.031 0.001 TRP F 610 HIS 0.011 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00321 (16372) covalent geometry : angle 0.61540 (22223) SS BOND : bond 0.00238 ( 35) SS BOND : angle 1.25501 ( 70) hydrogen bonds : bond 0.04838 ( 511) hydrogen bonds : angle 4.72277 ( 1335) link_ALPHA1-2 : bond 0.00215 ( 3) link_ALPHA1-2 : angle 1.98705 ( 9) link_ALPHA1-3 : bond 0.01162 ( 3) link_ALPHA1-3 : angle 1.39196 ( 9) link_BETA1-4 : bond 0.00377 ( 20) link_BETA1-4 : angle 1.80959 ( 60) link_BETA1-6 : bond 0.01920 ( 2) link_BETA1-6 : angle 3.22941 ( 6) link_NAG-ASN : bond 0.00580 ( 41) link_NAG-ASN : angle 2.70950 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 377 ASN cc_start: 0.8522 (t0) cc_final: 0.7944 (p0) REVERT: K 475 MET cc_start: 0.8109 (mmm) cc_final: 0.7787 (mmt) REVERT: J 631 TRP cc_start: 0.8124 (t-100) cc_final: 0.7915 (t-100) REVERT: C 180 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.7953 (t70) REVERT: C 482 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: D 648 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7685 (pt0) outliers start: 43 outliers final: 34 residues processed: 242 average time/residue: 0.1257 time to fit residues: 46.3064 Evaluate side-chains 236 residues out of total 1697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 131 CYS Chi-restraints excluded: chain K residue 272 ILE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 373 THR Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain J residue 621 GLU Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 122 optimal weight: 9.9990 chunk 118 optimal weight: 0.0270 chunk 93 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122139 restraints weight = 25195.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123044 restraints weight = 24685.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123940 restraints weight = 21845.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124192 restraints weight = 19014.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124239 restraints weight = 18305.795| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16476 Z= 0.127 Angle : 0.651 11.220 22500 Z= 0.316 Chirality : 0.046 0.278 2706 Planarity : 0.004 0.062 2727 Dihedral : 6.294 54.251 3459 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.42 % Allowed : 15.73 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.25 (0.19), residues: 1868 helix: 1.52 (0.27), residues: 432 sheet: 0.04 (0.22), residues: 530 loop : -0.33 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 503 TYR 0.013 0.001 TYR J 638 PHE 0.014 0.001 PHE B 71 TRP 0.037 0.001 TRP F 631 HIS 0.011 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00287 (16372) covalent geometry : angle 0.61047 (22223) SS BOND : bond 0.00205 ( 35) SS BOND : angle 1.19981 ( 70) hydrogen bonds : bond 0.04548 ( 511) hydrogen bonds : angle 4.60548 ( 1335) link_ALPHA1-2 : bond 0.00245 ( 3) link_ALPHA1-2 : angle 1.93746 ( 9) link_ALPHA1-3 : bond 0.01033 ( 3) link_ALPHA1-3 : angle 1.42210 ( 9) link_BETA1-4 : bond 0.00390 ( 20) link_BETA1-4 : angle 1.72313 ( 60) link_BETA1-6 : bond 0.02074 ( 2) link_BETA1-6 : angle 3.31076 ( 6) link_NAG-ASN : bond 0.00553 ( 41) link_NAG-ASN : angle 2.63339 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.34 seconds wall clock time: 40 minutes 52.62 seconds (2452.62 seconds total)