Starting phenix.real_space_refine on Fri Aug 7 07:46:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yig_72989/08_2026/9yig_72989.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yig_72989/08_2026/9yig_72989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yig_72989/08_2026/9yig_72989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yig_72989/08_2026/9yig_72989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yig_72989/08_2026/9yig_72989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yig_72989/08_2026/9yig_72989.map" } resolution = 3.4 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= 0.012 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 123 5.16 5 C 12374 2.51 5 N 3310 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19747 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "F" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "G" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3445 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 4 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "J" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "K" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 10, 'TRANS': 101} Chain: "L" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 10, 'TRANS': 101} Chain: "M" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 10, 'TRANS': 101} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" 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: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 3.94, per 1000 atoms: 0.20 Number of scatterers: 19747 At special positions: 0 Unit cell: (173.13, 172.26, 130.5, 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 123 16.00 O 3940 8.00 N 3310 7.00 C 12374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " 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=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN E 262 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 230 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 276 " " NAG E 609 " - " ASN E 295 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 339 " " NAG E 612 " - " ASN E 344 " " NAG E 613 " - " ASN E 386 " " NAG E 614 " - " ASN E 392 " " NAG E 615 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 230 " " NAG F 607 " - " ASN F 234 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 339 " " NAG F 612 " - " ASN F 344 " " NAG F 613 " - " ASN F 386 " " NAG F 614 " - " ASN F 392 " " NAG F 615 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 160 " " NAG G 605 " - " ASN G 197 " " NAG G 606 " - " ASN G 230 " " NAG G 607 " - " ASN G 234 " " NAG G 608 " - " ASN G 276 " " NAG G 609 " - " ASN G 295 " " NAG G 610 " - " ASN G 301 " " NAG G 611 " - " ASN G 339 " " NAG G 612 " - " ASN G 344 " " NAG G 613 " - " ASN G 386 " " NAG G 614 " - " ASN G 392 " " NAG G 615 " - " ASN G 448 " " NAG I 1 " - " ASN E 332 " " NAG O 1 " - " ASN F 262 " " NAG P 1 " - " ASN F 332 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 332 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 766.8 milliseconds 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 48 sheets defined 18.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.933A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 651 removed outlier: 4.099A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.716A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.933A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 651 removed outlier: 4.101A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.716A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.933A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 651 removed outlier: 4.100A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.717A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.672A 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: 3.554A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.096A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.671A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.555A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.096A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.671A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.555A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.095A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.528A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 64 removed outlier: 3.528A pdb=" N LYS J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.527A pdb=" N LYS M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 609 removed outlier: 7.263A pdb=" N THR A 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL E 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL A 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 604 through 609 removed outlier: 7.266A pdb=" N THR B 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL F 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL B 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 604 through 609 removed outlier: 7.266A pdb=" N THR C 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL G 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL C 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.908A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.265A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AA7, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AA9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.857A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.354A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.995A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.781A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.909A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.266A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AB7, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AB8, first strand: chain 'F' and resid 158 through 162 Processing sheet with id=AB9, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.858A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.354A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.995A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 301 through 308 removed outlier: 6.780A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.908A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.265A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AC9, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.857A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.353A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.995A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 301 through 308 removed outlier: 6.781A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.778A pdb=" N GLY H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.778A pdb=" N GLY H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR H 102 " --> pdb=" O THR H 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 6 through 7 Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.779A pdb=" N GLY J 10 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP J 35A" --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.779A pdb=" N GLY J 10 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.943A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE3, first strand: chain 'K' and resid 53 through 54 removed outlier: 5.569A pdb=" N ARG K 46 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU K 37 " --> pdb=" O ARG K 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.943A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AE6, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.569A pdb=" N ARG L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 6 through 7 Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.778A pdb=" N GLY M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP M 35A" --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.778A pdb=" N GLY M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR M 102 " --> pdb=" O THR M 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.943A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.569A pdb=" N ARG N 46 " --> pdb=" O LEU N 37 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU N 37 " --> pdb=" O ARG N 46 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6228 1.34 - 1.46: 4389 1.46 - 1.58: 9382 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 20161 Sorted by residual: bond pdb=" C1 MAN O 4 " pdb=" O5 MAN O 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C1 MAN Q 4 " pdb=" O5 MAN Q 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" CA GLY G 324 " pdb=" C GLY G 324 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.61e+00 bond pdb=" CA GLY F 324 " pdb=" C GLY F 324 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.59e+00 ... (remaining 20156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 26670 1.83 - 3.67: 642 3.67 - 5.50: 73 5.50 - 7.33: 6 7.33 - 9.17: 9 Bond angle restraints: 27400 Sorted by residual: angle pdb=" N ILE N 27B" pdb=" CA ILE N 27B" pdb=" C ILE N 27B" ideal model delta sigma weight residual 111.77 107.90 3.87 1.04e+00 9.25e-01 1.38e+01 angle pdb=" N ILE L 27B" pdb=" CA ILE L 27B" pdb=" C ILE L 27B" ideal model delta sigma weight residual 111.77 107.91 3.86 1.04e+00 9.25e-01 1.38e+01 angle pdb=" N ILE K 27B" pdb=" CA ILE K 27B" pdb=" C ILE K 27B" ideal model delta sigma weight residual 111.77 107.92 3.85 1.04e+00 9.25e-01 1.37e+01 angle pdb=" N SER J 31 " pdb=" CA SER J 31 " pdb=" C SER J 31 " ideal model delta sigma weight residual 108.23 112.80 -4.57 1.38e+00 5.25e-01 1.10e+01 angle pdb=" N SER M 31 " pdb=" CA SER M 31 " pdb=" C SER M 31 " ideal model delta sigma weight residual 108.23 112.78 -4.55 1.38e+00 5.25e-01 1.09e+01 ... (remaining 27395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 11901 21.64 - 43.28: 988 43.28 - 64.91: 90 64.91 - 86.55: 57 86.55 - 108.19: 27 Dihedral angle restraints: 13063 sinusoidal: 6181 harmonic: 6882 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.18 -58.18 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.14 -58.14 1 1.00e+01 1.00e-02 4.53e+01 ... (remaining 13060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3179 0.113 - 0.225: 96 0.225 - 0.338: 9 0.338 - 0.451: 0 0.451 - 0.564: 6 Chirality restraints: 3290 Sorted by residual: chirality pdb=" C1 NAG F 602 " pdb=" ND2 ASN F 133 " pdb=" C2 NAG F 602 " pdb=" O5 NAG F 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG G 602 " pdb=" ND2 ASN G 133 " pdb=" C2 NAG G 602 " pdb=" O5 NAG G 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 3287 not shown) Planarity restraints: 3448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 7 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO N 8 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 7 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO K 8 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO K 8 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO K 8 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO L 8 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.016 5.00e-02 4.00e+02 ... (remaining 3445 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 11032 3.02 - 3.49: 18554 3.49 - 3.96: 30632 3.96 - 4.43: 34933 4.43 - 4.90: 57256 Nonbonded interactions: 152407 Sorted by model distance: nonbonded pdb=" NH2 ARG F 327 " pdb=" CE1 TYR J 33 " model vdw 2.550 3.420 nonbonded pdb=" NH2 ARG E 327 " pdb=" CE1 TYR M 33 " model vdw 2.554 3.420 nonbonded pdb=" NH2 ARG G 327 " pdb=" CE1 TYR H 33 " model vdw 2.557 3.420 nonbonded pdb=" O SER M 31 " pdb=" OG1 THR M 32 " model vdw 2.626 3.040 nonbonded pdb=" O SER H 31 " pdb=" OG1 THR H 32 " model vdw 2.626 3.040 ... (remaining 152402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = (chain 'E' and resid 34 through 615) selection = (chain 'F' and resid 34 through 615) selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 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 : 0.004 0.033 20278 Z= 0.203 Angle : 0.703 18.553 27709 Z= 0.303 Chirality : 0.055 0.564 3290 Planarity : 0.003 0.029 3394 Dihedral : 15.906 108.188 8517 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.14 % Allowed : 5.17 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2333 helix: 1.33 (0.28), residues: 408 sheet: -0.12 (0.21), residues: 612 loop : -1.12 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 273 TYR 0.012 0.001 TYR E 134 PHE 0.007 0.001 PHE F 53 TRP 0.006 0.001 TRP J 35A HIS 0.002 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (20161) covalent geometry : angle 0.61639 / 0.28 (27400) SS BOND : bond 0.00353 / 0.21 ( 42) SS BOND : angle 0.57784 / 0.43 ( 84) hydrogen bonds : bond 0.13285 / 9.01 ( 606) hydrogen bonds : angle 5.65149 / 3.96 ( 1683) link_ALPHA1-3 : bond 0.00710 / 0.40 ( 6) link_ALPHA1-3 : angle 2.93653 / 1.85 ( 18) link_ALPHA1-6 : bond 0.00284 / 0.14 ( 3) link_ALPHA1-6 : angle 0.44501 / 0.23 ( 9) link_BETA1-4 : bond 0.00511 / 0.30 ( 12) link_BETA1-4 : angle 1.99907 / 1.18 ( 36) link_NAG-ASN : bond 0.00671 / 0.48 ( 54) link_NAG-ASN : angle 4.28250 / 2.92 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 400 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.7762 (m-40) cc_final: 0.7552 (m-40) REVERT: E 348 GLN cc_start: 0.8126 (tp40) cc_final: 0.7583 (tp40) REVERT: E 484 TYR cc_start: 0.8436 (p90) cc_final: 0.8063 (p90) REVERT: F 46 LYS cc_start: 0.8579 (ptmt) cc_final: 0.7846 (ptpt) REVERT: F 106 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7793 (mt-10) REVERT: F 117 LYS cc_start: 0.8316 (ttmm) cc_final: 0.8067 (tttt) REVERT: F 207 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7514 (tptt) REVERT: F 492 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7426 (mt-10) REVERT: G 46 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7776 (pttt) REVERT: G 83 GLU cc_start: 0.7890 (tt0) cc_final: 0.7685 (tp30) REVERT: G 161 MET cc_start: 0.7903 (tpt) cc_final: 0.7512 (tpt) REVERT: G 207 LYS cc_start: 0.7830 (mmtm) cc_final: 0.6984 (tptp) REVERT: G 326 ILE cc_start: 0.7545 (mp) cc_final: 0.6971 (tt) REVERT: G 484 TYR cc_start: 0.8735 (p90) cc_final: 0.8321 (p90) REVERT: G 496 VAL cc_start: 0.8363 (m) cc_final: 0.7905 (m) REVERT: H 72 ASP cc_start: 0.7346 (p0) cc_final: 0.7057 (p0) REVERT: J 98 ASP cc_start: 0.5153 (p0) cc_final: 0.4502 (p0) REVERT: M 77 HIS cc_start: 0.4936 (m-70) cc_final: 0.4734 (m-70) outliers start: 3 outliers final: 0 residues processed: 403 average time/residue: 0.1135 time to fit residues: 73.7864 Evaluate side-chains 265 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.0970 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN B 543 ASN B 650 GLN C 650 GLN E 99 ASN E 103 GLN E 114 GLN F 99 ASN F 103 GLN F 114 GLN F 440 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 103 GLN G 114 GLN G 330 HIS K 27DHIS L 27DHIS N 27DHIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.183556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134022 restraints weight = 27321.540| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.26 r_work: 0.3477 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20278 Z= 0.161 Angle : 0.687 17.499 27709 Z= 0.323 Chirality : 0.051 0.550 3290 Planarity : 0.004 0.065 3394 Dihedral : 9.543 69.551 4115 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.04 % Rotamer: Outliers : 1.99 % Allowed : 13.33 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2333 helix: 1.42 (0.27), residues: 413 sheet: 0.11 (0.21), residues: 599 loop : -1.24 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 178 TYR 0.020 0.002 TYR J 50 PHE 0.017 0.002 PHE H 91 TRP 0.013 0.001 TRP C 631 HIS 0.008 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (20161) covalent geometry : angle 0.59314 / 0.30 (27400) SS BOND : bond 0.00473 / 0.29 ( 42) SS BOND : angle 1.70544 / 1.21 ( 84) hydrogen bonds : bond 0.03490 / 2.33 ( 606) hydrogen bonds : angle 4.60896 / 3.28 ( 1683) link_ALPHA1-3 : bond 0.01673 / 0.94 ( 6) link_ALPHA1-3 : angle 2.89402 / 1.72 ( 18) link_ALPHA1-6 : bond 0.00131 / 0.06 ( 3) link_ALPHA1-6 : angle 2.22216 / 1.23 ( 9) link_BETA1-4 : bond 0.00539 / 0.32 ( 12) link_BETA1-4 : angle 1.69498 / 1.04 ( 36) link_NAG-ASN : bond 0.00603 / 0.43 ( 54) link_NAG-ASN : angle 4.23800 / 2.89 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7399 (mt-10) REVERT: B 543 ASN cc_start: 0.7859 (t0) cc_final: 0.7502 (t0) REVERT: B 634 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: E 348 GLN cc_start: 0.7843 (tp40) cc_final: 0.7050 (tp40) REVERT: E 484 TYR cc_start: 0.8506 (p90) cc_final: 0.8164 (p90) REVERT: F 46 LYS cc_start: 0.8365 (ptmt) cc_final: 0.7737 (ptpp) REVERT: F 99 ASN cc_start: 0.7594 (t0) cc_final: 0.7358 (t0) REVERT: F 106 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7700 (mt-10) REVERT: F 117 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8033 (tttt) REVERT: F 207 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7604 (tptt) REVERT: F 231 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8224 (ttmm) REVERT: F 300 ASN cc_start: 0.8268 (p0) cc_final: 0.7998 (p0) REVERT: F 335 LYS cc_start: 0.7817 (tptm) cc_final: 0.7557 (tttp) REVERT: G 46 LYS cc_start: 0.8145 (ptmt) cc_final: 0.7469 (pttt) REVERT: G 83 GLU cc_start: 0.8146 (tt0) cc_final: 0.7707 (tp30) REVERT: G 207 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7109 (tptp) REVERT: G 326 ILE cc_start: 0.7709 (mp) cc_final: 0.7105 (tt) REVERT: G 484 TYR cc_start: 0.8695 (p90) cc_final: 0.8047 (p90) REVERT: H 72 ASP cc_start: 0.5937 (p0) cc_final: 0.5732 (p0) REVERT: J 53 TYR cc_start: 0.6367 (p90) cc_final: 0.5981 (p90) REVERT: L 34 SER cc_start: 0.8848 (m) cc_final: 0.8556 (m) outliers start: 42 outliers final: 21 residues processed: 302 average time/residue: 0.1105 time to fit residues: 54.0665 Evaluate side-chains 274 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 116 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 230 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN C 543 ASN E 105 HIS F 330 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27DHIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128619 restraints weight = 27445.229| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.44 r_work: 0.3404 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20278 Z= 0.180 Angle : 0.698 17.474 27709 Z= 0.328 Chirality : 0.051 0.540 3290 Planarity : 0.004 0.062 3394 Dihedral : 8.204 58.326 4115 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.30 % Rotamer: Outliers : 2.61 % Allowed : 16.08 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2333 helix: 1.15 (0.27), residues: 414 sheet: 0.15 (0.21), residues: 598 loop : -1.32 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.018 0.001 TYR J 50 PHE 0.016 0.002 PHE E 223 TRP 0.011 0.001 TRP G 427 HIS 0.008 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (20161) covalent geometry : angle 0.60524 / 0.31 (27400) SS BOND : bond 0.00449 / 0.29 ( 42) SS BOND : angle 1.86570 / 1.30 ( 84) hydrogen bonds : bond 0.03745 / 2.46 ( 606) hydrogen bonds : angle 4.65182 / 3.31 ( 1683) link_ALPHA1-3 : bond 0.01688 / 0.92 ( 6) link_ALPHA1-3 : angle 2.30325 / 1.38 ( 18) link_ALPHA1-6 : bond 0.00156 / 0.08 ( 3) link_ALPHA1-6 : angle 1.96730 / 1.13 ( 9) link_BETA1-4 : bond 0.00577 / 0.34 ( 12) link_BETA1-4 : angle 1.27160 / 0.76 ( 36) link_NAG-ASN : bond 0.00608 / 0.42 ( 54) link_NAG-ASN : angle 4.29689 / 3.08 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8153 (t0) cc_final: 0.7934 (t0) REVERT: A 584 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7835 (tm-30) REVERT: B 536 THR cc_start: 0.7997 (t) cc_final: 0.7783 (m) REVERT: B 543 ASN cc_start: 0.7922 (t0) cc_final: 0.7504 (t0) REVERT: B 633 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7493 (mmtm) REVERT: B 634 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: E 348 GLN cc_start: 0.7932 (tp40) cc_final: 0.7081 (tp40) REVERT: E 393 SER cc_start: 0.7788 (m) cc_final: 0.7376 (p) REVERT: F 46 LYS cc_start: 0.8316 (ptmt) cc_final: 0.8035 (mmtt) REVERT: F 106 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7750 (mt-10) REVERT: F 117 LYS cc_start: 0.8337 (ttmm) cc_final: 0.8079 (tttt) REVERT: F 207 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7654 (tptt) REVERT: F 231 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8192 (ttmm) REVERT: F 300 ASN cc_start: 0.8707 (p0) cc_final: 0.8440 (p0) REVERT: F 492 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8203 (mm-30) REVERT: G 207 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7418 (tptp) REVERT: G 300 ASN cc_start: 0.8732 (p0) cc_final: 0.8459 (p0) REVERT: G 326 ILE cc_start: 0.7611 (mp) cc_final: 0.7106 (tt) REVERT: G 484 TYR cc_start: 0.8591 (p90) cc_final: 0.8076 (p90) REVERT: G 492 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7688 (mm-30) REVERT: L 34 SER cc_start: 0.8821 (m) cc_final: 0.8493 (m) REVERT: M 50 TYR cc_start: 0.7264 (p90) cc_final: 0.6963 (p90) outliers start: 55 outliers final: 41 residues processed: 294 average time/residue: 0.1047 time to fit residues: 50.8725 Evaluate side-chains 280 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 160 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 330 HIS ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.179210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128463 restraints weight = 27370.718| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.49 r_work: 0.3410 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20278 Z= 0.157 Angle : 0.661 16.639 27709 Z= 0.310 Chirality : 0.051 0.548 3290 Planarity : 0.003 0.061 3394 Dihedral : 7.114 49.378 4115 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 2.85 % Allowed : 17.84 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2333 helix: 1.24 (0.27), residues: 417 sheet: 0.15 (0.21), residues: 608 loop : -1.32 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 350 TYR 0.018 0.001 TYR J 50 PHE 0.017 0.002 PHE G 53 TRP 0.011 0.001 TRP G 427 HIS 0.004 0.001 HIS K 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (20161) covalent geometry : angle 0.57358 / 0.29 (27400) SS BOND : bond 0.00456 / 0.31 ( 42) SS BOND : angle 1.66253 / 1.08 ( 84) hydrogen bonds : bond 0.03353 / 2.20 ( 606) hydrogen bonds : angle 4.53569 / 3.23 ( 1683) link_ALPHA1-3 : bond 0.01605 / 0.90 ( 6) link_ALPHA1-3 : angle 2.12268 / 1.22 ( 18) link_ALPHA1-6 : bond 0.00040 / 0.02 ( 3) link_ALPHA1-6 : angle 2.65037 / 1.44 ( 9) link_BETA1-4 : bond 0.00500 / 0.29 ( 12) link_BETA1-4 : angle 1.58485 / 1.02 ( 36) link_NAG-ASN : bond 0.00566 / 0.40 ( 54) link_NAG-ASN : angle 4.02589 / 2.85 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8093 (t0) cc_final: 0.7844 (t0) REVERT: A 584 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7811 (tm-30) REVERT: B 536 THR cc_start: 0.7950 (t) cc_final: 0.7743 (m) REVERT: B 543 ASN cc_start: 0.7756 (t0) cc_final: 0.7254 (t0) REVERT: B 634 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: C 535 MET cc_start: 0.7676 (mtp) cc_final: 0.7431 (mtt) REVERT: C 604 CYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7352 (p) REVERT: E 116 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7598 (mp) REVERT: E 348 GLN cc_start: 0.7930 (tp40) cc_final: 0.7070 (tp40) REVERT: E 393 SER cc_start: 0.7939 (m) cc_final: 0.7525 (p) REVERT: E 444 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7017 (tmm160) REVERT: F 46 LYS cc_start: 0.8269 (ptmt) cc_final: 0.8040 (mmtt) REVERT: F 106 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7763 (mt-10) REVERT: F 207 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7647 (tptt) REVERT: F 231 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8163 (mttm) REVERT: F 300 ASN cc_start: 0.8844 (p0) cc_final: 0.8538 (p0) REVERT: F 416 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8429 (mt) REVERT: F 492 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8096 (mm-30) REVERT: G 207 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7675 (tptt) REVERT: G 300 ASN cc_start: 0.8720 (p0) cc_final: 0.8428 (p0) REVERT: G 326 ILE cc_start: 0.7667 (mp) cc_final: 0.7191 (tt) REVERT: G 484 TYR cc_start: 0.8654 (p90) cc_final: 0.8053 (p90) REVERT: G 492 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7731 (mm-30) outliers start: 60 outliers final: 39 residues processed: 275 average time/residue: 0.1280 time to fit residues: 57.9289 Evaluate side-chains 268 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 48 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.180263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129183 restraints weight = 27399.964| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.59 r_work: 0.3419 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20278 Z= 0.127 Angle : 0.631 16.000 27709 Z= 0.297 Chirality : 0.050 0.537 3290 Planarity : 0.003 0.056 3394 Dihedral : 6.509 49.998 4115 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 3.56 % Allowed : 18.31 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2333 helix: 1.39 (0.27), residues: 416 sheet: 0.26 (0.21), residues: 588 loop : -1.28 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 166 TYR 0.028 0.001 TYR M 50 PHE 0.011 0.001 PHE E 223 TRP 0.010 0.001 TRP G 427 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (20161) covalent geometry : angle 0.54672 / 0.28 (27400) SS BOND : bond 0.00424 / 0.27 ( 42) SS BOND : angle 1.68601 / 1.22 ( 84) hydrogen bonds : bond 0.03145 / 2.07 ( 606) hydrogen bonds : angle 4.40857 / 3.14 ( 1683) link_ALPHA1-3 : bond 0.01498 / 0.82 ( 6) link_ALPHA1-3 : angle 2.30457 / 1.35 ( 18) link_ALPHA1-6 : bond 0.00162 / 0.08 ( 3) link_ALPHA1-6 : angle 2.32183 / 1.28 ( 9) link_BETA1-4 : bond 0.00516 / 0.30 ( 12) link_BETA1-4 : angle 1.67652 / 1.08 ( 36) link_NAG-ASN : bond 0.00581 / 0.41 ( 54) link_NAG-ASN : angle 3.81377 / 2.67 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8099 (t0) cc_final: 0.7816 (t0) REVERT: B 543 ASN cc_start: 0.7820 (t0) cc_final: 0.7300 (t0) REVERT: B 634 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: C 535 MET cc_start: 0.7764 (mtp) cc_final: 0.7538 (mtt) REVERT: C 604 CYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7538 (p) REVERT: E 278 THR cc_start: 0.8750 (m) cc_final: 0.8460 (p) REVERT: E 348 GLN cc_start: 0.7878 (tp40) cc_final: 0.6972 (tp40) REVERT: E 393 SER cc_start: 0.7986 (m) cc_final: 0.7564 (p) REVERT: E 444 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.6758 (tmm160) REVERT: E 484 TYR cc_start: 0.8644 (p90) cc_final: 0.8389 (p90) REVERT: E 492 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7906 (mm-30) REVERT: F 106 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7781 (mt-10) REVERT: F 207 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7627 (tptt) REVERT: F 300 ASN cc_start: 0.8880 (p0) cc_final: 0.8561 (p0) REVERT: G 207 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7668 (tptt) REVERT: G 300 ASN cc_start: 0.8679 (p0) cc_final: 0.8400 (p0) REVERT: G 326 ILE cc_start: 0.7745 (mp) cc_final: 0.7317 (tt) REVERT: G 484 TYR cc_start: 0.8620 (p90) cc_final: 0.7936 (p90) REVERT: G 492 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7748 (mm-30) REVERT: L 87 TYR cc_start: 0.7251 (m-10) cc_final: 0.6881 (m-10) outliers start: 75 outliers final: 53 residues processed: 280 average time/residue: 0.1170 time to fit residues: 54.5594 Evaluate side-chains 275 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 124 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 GLN C 577 GLN E 85 HIS ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 HIS N 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.172157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117641 restraints weight = 27763.737| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.19 r_work: 0.3329 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20278 Z= 0.266 Angle : 0.769 16.123 27709 Z= 0.368 Chirality : 0.053 0.517 3290 Planarity : 0.004 0.060 3394 Dihedral : 7.327 53.189 4115 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.37 % Rotamer: Outliers : 4.03 % Allowed : 19.78 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2333 helix: 0.83 (0.26), residues: 417 sheet: -0.05 (0.21), residues: 568 loop : -1.43 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 444 TYR 0.017 0.002 TYR F 484 PHE 0.018 0.002 PHE G 53 TRP 0.021 0.002 TRP G 427 HIS 0.007 0.001 HIS K 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.27 (20161) covalent geometry : angle 0.69333 / 0.35 (27400) SS BOND : bond 0.00574 / 0.36 ( 42) SS BOND : angle 2.03743 / 1.42 ( 84) hydrogen bonds : bond 0.04090 / 2.74 ( 606) hydrogen bonds : angle 4.76087 / 3.38 ( 1683) link_ALPHA1-3 : bond 0.01253 / 0.69 ( 6) link_ALPHA1-3 : angle 2.53714 / 1.51 ( 18) link_ALPHA1-6 : bond 0.00254 / 0.13 ( 3) link_ALPHA1-6 : angle 2.92192 / 1.62 ( 9) link_BETA1-4 : bond 0.00660 / 0.39 ( 12) link_BETA1-4 : angle 1.62512 / 1.01 ( 36) link_NAG-ASN : bond 0.00581 / 0.38 ( 54) link_NAG-ASN : angle 4.00235 / 2.79 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 222 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8073 (t0) cc_final: 0.7785 (t0) REVERT: B 545 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8206 (tt) REVERT: B 633 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7684 (mmtm) REVERT: B 634 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: C 535 MET cc_start: 0.7851 (mtp) cc_final: 0.7610 (mtt) REVERT: C 543 ASN cc_start: 0.7941 (t0) cc_final: 0.7595 (t0) REVERT: C 604 CYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7894 (p) REVERT: E 116 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8021 (mp) REVERT: E 142 MET cc_start: 0.6778 (ttm) cc_final: 0.5721 (ttm) REVERT: E 207 LYS cc_start: 0.8319 (mmtm) cc_final: 0.7725 (tptt) REVERT: E 444 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7009 (tmm160) REVERT: F 106 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7831 (mt-10) REVERT: F 207 LYS cc_start: 0.8349 (mmtm) cc_final: 0.7910 (tptt) REVERT: F 363 GLN cc_start: 0.8082 (pt0) cc_final: 0.7818 (pm20) REVERT: F 416 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8454 (mt) REVERT: G 96 TRP cc_start: 0.8598 (m100) cc_final: 0.8306 (m100) REVERT: G 104 MET cc_start: 0.8853 (ttt) cc_final: 0.8626 (ttt) REVERT: G 207 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7924 (tptt) REVERT: G 326 ILE cc_start: 0.7795 (mp) cc_final: 0.7350 (tt) REVERT: G 363 GLN cc_start: 0.7951 (pt0) cc_final: 0.7691 (pt0) REVERT: G 484 TYR cc_start: 0.8649 (p90) cc_final: 0.7982 (p90) REVERT: G 492 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8048 (mt-10) REVERT: H 57 THR cc_start: 0.7304 (p) cc_final: 0.6965 (p) outliers start: 85 outliers final: 61 residues processed: 281 average time/residue: 0.1242 time to fit residues: 56.9860 Evaluate side-chains 276 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 209 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 171 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 190 optimal weight: 30.0000 chunk 180 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN B 652 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.170351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116143 restraints weight = 27888.775| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.18 r_work: 0.3312 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 20278 Z= 0.287 Angle : 0.775 15.804 27709 Z= 0.374 Chirality : 0.054 0.502 3290 Planarity : 0.004 0.060 3394 Dihedral : 7.560 59.551 4115 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 3.94 % Allowed : 21.20 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2333 helix: 0.75 (0.26), residues: 405 sheet: -0.21 (0.21), residues: 568 loop : -1.57 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 617 TYR 0.021 0.002 TYR M 50 PHE 0.018 0.002 PHE G 53 TRP 0.017 0.002 TRP G 427 HIS 0.007 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.29 (20161) covalent geometry : angle 0.70233 / 0.36 (27400) SS BOND : bond 0.00587 / 0.37 ( 42) SS BOND : angle 1.78162 / 1.24 ( 84) hydrogen bonds : bond 0.04051 / 2.70 ( 606) hydrogen bonds : angle 4.82309 / 3.44 ( 1683) link_ALPHA1-3 : bond 0.01250 / 0.70 ( 6) link_ALPHA1-3 : angle 2.64063 / 1.55 ( 18) link_ALPHA1-6 : bond 0.00300 / 0.15 ( 3) link_ALPHA1-6 : angle 2.76275 / 1.54 ( 9) link_BETA1-4 : bond 0.00624 / 0.37 ( 12) link_BETA1-4 : angle 1.64954 / 1.06 ( 36) link_NAG-ASN : bond 0.00558 / 0.36 ( 54) link_NAG-ASN : angle 3.97910 / 2.76 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 211 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: B 633 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7681 (mmtm) REVERT: C 535 MET cc_start: 0.8057 (mtp) cc_final: 0.7843 (mtt) REVERT: C 604 CYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7860 (p) REVERT: C 652 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.5470 (mm-40) REVERT: E 116 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8092 (mp) REVERT: E 142 MET cc_start: 0.6830 (ttm) cc_final: 0.5827 (ttm) REVERT: E 207 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7873 (tptt) REVERT: E 444 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.6969 (tmm160) REVERT: F 106 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7846 (mt-10) REVERT: F 207 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7942 (tptt) REVERT: F 231 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8272 (mttm) REVERT: F 363 GLN cc_start: 0.8109 (pt0) cc_final: 0.7877 (pm20) REVERT: F 416 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8441 (mt) REVERT: G 104 MET cc_start: 0.8880 (ttt) cc_final: 0.8656 (ttt) REVERT: G 207 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8006 (tptt) REVERT: G 363 GLN cc_start: 0.8054 (pt0) cc_final: 0.7787 (pt0) REVERT: G 492 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8037 (mt-10) REVERT: H 57 THR cc_start: 0.7374 (p) cc_final: 0.7002 (p) outliers start: 83 outliers final: 67 residues processed: 270 average time/residue: 0.1197 time to fit residues: 52.5419 Evaluate side-chains 273 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 201 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 652 GLN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 360 ARG Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 429 ARG Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 132 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 135 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120337 restraints weight = 27753.039| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.20 r_work: 0.3367 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20278 Z= 0.142 Angle : 0.671 14.527 27709 Z= 0.319 Chirality : 0.050 0.500 3290 Planarity : 0.004 0.089 3394 Dihedral : 7.021 58.006 4115 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.61 % Allowed : 22.15 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2333 helix: 1.01 (0.27), residues: 417 sheet: -0.09 (0.21), residues: 558 loop : -1.42 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 617 TYR 0.028 0.001 TYR M 50 PHE 0.014 0.001 PHE E 468 TRP 0.012 0.001 TRP G 112 HIS 0.004 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (20161) covalent geometry : angle 0.59683 / 0.30 (27400) SS BOND : bond 0.00448 / 0.29 ( 42) SS BOND : angle 1.65606 / 1.21 ( 84) hydrogen bonds : bond 0.03383 / 2.24 ( 606) hydrogen bonds : angle 4.56315 / 3.25 ( 1683) link_ALPHA1-3 : bond 0.01207 / 0.66 ( 6) link_ALPHA1-3 : angle 2.51648 / 1.48 ( 18) link_ALPHA1-6 : bond 0.00145 / 0.07 ( 3) link_ALPHA1-6 : angle 2.24555 / 1.25 ( 9) link_BETA1-4 : bond 0.00491 / 0.29 ( 12) link_BETA1-4 : angle 1.56506 / 1.01 ( 36) link_NAG-ASN : bond 0.00534 / 0.37 ( 54) link_NAG-ASN : angle 3.72836 / 2.58 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 224 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: B 633 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7638 (mmtm) REVERT: C 535 MET cc_start: 0.8033 (mtp) cc_final: 0.7825 (mtt) REVERT: C 604 CYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8024 (p) REVERT: E 96 TRP cc_start: 0.8471 (m100) cc_final: 0.8207 (m100) REVERT: E 106 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7788 (mt-10) REVERT: E 142 MET cc_start: 0.6670 (ttm) cc_final: 0.5724 (ttm) REVERT: E 207 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7730 (tptt) REVERT: E 348 GLN cc_start: 0.8047 (tp40) cc_final: 0.7173 (tp40) REVERT: E 444 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.6868 (tmm160) REVERT: F 106 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7817 (mt-10) REVERT: F 142 MET cc_start: 0.6523 (ttt) cc_final: 0.6050 (ttm) REVERT: F 207 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7824 (tptt) REVERT: F 416 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8454 (mt) REVERT: G 96 TRP cc_start: 0.8602 (m100) cc_final: 0.8302 (m100) REVERT: G 207 LYS cc_start: 0.8404 (mmtm) cc_final: 0.7955 (tptt) REVERT: G 300 ASN cc_start: 0.8809 (p0) cc_final: 0.8569 (p0) REVERT: G 326 ILE cc_start: 0.7993 (mp) cc_final: 0.7434 (tt) REVERT: G 363 GLN cc_start: 0.7944 (pt0) cc_final: 0.7672 (pt0) REVERT: G 492 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7898 (mt-10) REVERT: H 57 THR cc_start: 0.7248 (p) cc_final: 0.6883 (p) REVERT: N 34 SER cc_start: 0.8674 (m) cc_final: 0.8380 (m) outliers start: 76 outliers final: 56 residues processed: 278 average time/residue: 0.1264 time to fit residues: 57.0123 Evaluate side-chains 271 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 360 ARG Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 86 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123633 restraints weight = 27635.415| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.66 r_work: 0.3380 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20278 Z= 0.140 Angle : 0.655 14.099 27709 Z= 0.312 Chirality : 0.050 0.481 3290 Planarity : 0.004 0.070 3394 Dihedral : 6.728 59.025 4115 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.42 % Allowed : 22.58 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2333 helix: 1.15 (0.27), residues: 417 sheet: -0.03 (0.21), residues: 556 loop : -1.37 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 178 TYR 0.023 0.001 TYR M 50 PHE 0.013 0.001 PHE F 53 TRP 0.014 0.001 TRP A 623 HIS 0.004 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (20161) covalent geometry : angle 0.58244 / 0.29 (27400) SS BOND : bond 0.00482 / 0.31 ( 42) SS BOND : angle 1.67580 / 1.22 ( 84) hydrogen bonds : bond 0.03292 / 2.18 ( 606) hydrogen bonds : angle 4.47461 / 3.19 ( 1683) link_ALPHA1-3 : bond 0.01197 / 0.66 ( 6) link_ALPHA1-3 : angle 2.53260 / 1.49 ( 18) link_ALPHA1-6 : bond 0.00192 / 0.10 ( 3) link_ALPHA1-6 : angle 2.25721 / 1.25 ( 9) link_BETA1-4 : bond 0.00516 / 0.31 ( 12) link_BETA1-4 : angle 1.63305 / 1.05 ( 36) link_NAG-ASN : bond 0.00515 / 0.35 ( 54) link_NAG-ASN : angle 3.60040 / 2.48 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 602 LEU cc_start: 0.7893 (mt) cc_final: 0.7637 (mt) REVERT: B 633 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7558 (mmtm) REVERT: C 604 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7846 (p) REVERT: C 634 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7086 (mt-10) REVERT: E 96 TRP cc_start: 0.8342 (m100) cc_final: 0.8027 (m100) REVERT: E 106 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7667 (mt-10) REVERT: E 142 MET cc_start: 0.6391 (ttm) cc_final: 0.5455 (ttm) REVERT: E 207 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7658 (tptt) REVERT: E 278 THR cc_start: 0.8812 (m) cc_final: 0.8496 (p) REVERT: E 348 GLN cc_start: 0.7941 (tp40) cc_final: 0.7028 (tp40) REVERT: E 373 THR cc_start: 0.8965 (p) cc_final: 0.8741 (t) REVERT: E 444 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.6914 (tmm160) REVERT: F 106 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7763 (mt-10) REVERT: F 142 MET cc_start: 0.6304 (ttt) cc_final: 0.5837 (ttm) REVERT: F 207 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7763 (tptt) REVERT: F 416 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8300 (mt) REVERT: G 96 TRP cc_start: 0.8512 (m100) cc_final: 0.8208 (m100) REVERT: G 207 LYS cc_start: 0.8395 (mmtm) cc_final: 0.7862 (tptt) REVERT: G 300 ASN cc_start: 0.8754 (p0) cc_final: 0.8465 (p0) REVERT: G 326 ILE cc_start: 0.7921 (mp) cc_final: 0.7385 (tt) REVERT: G 363 GLN cc_start: 0.7800 (pt0) cc_final: 0.7428 (pm20) REVERT: G 429 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8428 (ttm110) REVERT: G 484 TYR cc_start: 0.8433 (p90) cc_final: 0.8162 (p90) REVERT: G 492 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7832 (mt-10) REVERT: N 34 SER cc_start: 0.8728 (m) cc_final: 0.8425 (m) outliers start: 72 outliers final: 60 residues processed: 266 average time/residue: 0.1260 time to fit residues: 54.6906 Evaluate side-chains 276 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 360 ARG Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 429 ARG Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 102 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119785 restraints weight = 27679.875| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.15 r_work: 0.3363 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20278 Z= 0.172 Angle : 0.671 14.410 27709 Z= 0.321 Chirality : 0.050 0.491 3290 Planarity : 0.004 0.062 3394 Dihedral : 6.724 58.787 4115 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.51 % Allowed : 22.53 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2333 helix: 1.10 (0.27), residues: 417 sheet: -0.07 (0.21), residues: 556 loop : -1.39 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 178 TYR 0.024 0.002 TYR M 50 PHE 0.013 0.002 PHE F 53 TRP 0.015 0.001 TRP G 427 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (20161) covalent geometry : angle 0.60048 / 0.30 (27400) SS BOND : bond 0.00466 / 0.30 ( 42) SS BOND : angle 1.74669 / 1.26 ( 84) hydrogen bonds : bond 0.03454 / 2.30 ( 606) hydrogen bonds : angle 4.48752 / 3.20 ( 1683) link_ALPHA1-3 : bond 0.01188 / 0.67 ( 6) link_ALPHA1-3 : angle 2.54040 / 1.49 ( 18) link_ALPHA1-6 : bond 0.00115 / 0.06 ( 3) link_ALPHA1-6 : angle 2.37694 / 1.32 ( 9) link_BETA1-4 : bond 0.00546 / 0.32 ( 12) link_BETA1-4 : angle 1.60229 / 1.02 ( 36) link_NAG-ASN : bond 0.00513 / 0.35 ( 54) link_NAG-ASN : angle 3.59385 / 2.47 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 602 LEU cc_start: 0.7885 (mt) cc_final: 0.7636 (mt) REVERT: B 626 MET cc_start: 0.7990 (tpp) cc_final: 0.7226 (tpt) REVERT: B 633 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7514 (mmtm) REVERT: B 634 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7207 (mp0) REVERT: C 604 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7924 (p) REVERT: C 652 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.5962 (mm-40) REVERT: E 96 TRP cc_start: 0.8382 (m100) cc_final: 0.8079 (m100) REVERT: E 106 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7672 (mt-10) REVERT: E 142 MET cc_start: 0.6413 (ttm) cc_final: 0.5469 (ttm) REVERT: E 207 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7672 (tptt) REVERT: E 278 THR cc_start: 0.8821 (m) cc_final: 0.8494 (p) REVERT: E 348 GLN cc_start: 0.8077 (tp40) cc_final: 0.7147 (tp40) REVERT: E 373 THR cc_start: 0.9011 (p) cc_final: 0.8780 (t) REVERT: E 444 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.6944 (tmm160) REVERT: F 106 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7697 (mt-10) REVERT: F 142 MET cc_start: 0.6377 (ttt) cc_final: 0.5902 (ttm) REVERT: F 207 LYS cc_start: 0.8298 (mmtm) cc_final: 0.7768 (tptt) REVERT: F 416 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8335 (mt) REVERT: G 96 TRP cc_start: 0.8545 (m100) cc_final: 0.8246 (m100) REVERT: G 207 LYS cc_start: 0.8406 (mmtm) cc_final: 0.7887 (tptt) REVERT: G 300 ASN cc_start: 0.8814 (p0) cc_final: 0.8539 (p0) REVERT: G 326 ILE cc_start: 0.7901 (mp) cc_final: 0.7370 (tt) REVERT: G 363 GLN cc_start: 0.7843 (pt0) cc_final: 0.7461 (pm20) REVERT: G 484 TYR cc_start: 0.8474 (p90) cc_final: 0.8210 (p90) REVERT: G 492 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7776 (mt-10) REVERT: H 57 THR cc_start: 0.7216 (p) cc_final: 0.6858 (p) REVERT: N 34 SER cc_start: 0.8810 (m) cc_final: 0.8481 (m) outliers start: 74 outliers final: 60 residues processed: 263 average time/residue: 0.1306 time to fit residues: 55.8394 Evaluate side-chains 266 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 202 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 652 GLN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 429 ARG Chi-restraints excluded: chain G residue 440 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 86 TYR Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 206 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 121 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 226 optimal weight: 0.0070 chunk 99 optimal weight: 0.0000 chunk 60 optimal weight: 0.5980 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128930 restraints weight = 27289.687| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.50 r_work: 0.3415 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20278 Z= 0.103 Angle : 0.615 13.275 27709 Z= 0.294 Chirality : 0.048 0.476 3290 Planarity : 0.003 0.053 3394 Dihedral : 6.041 50.312 4115 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.56 % Allowed : 23.43 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2333 helix: 1.50 (0.28), residues: 414 sheet: 0.14 (0.21), residues: 558 loop : -1.26 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 46 TYR 0.026 0.001 TYR M 50 PHE 0.013 0.001 PHE H 91 TRP 0.012 0.001 TRP G 112 HIS 0.003 0.001 HIS F 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (20161) covalent geometry : angle 0.54974 / 0.28 (27400) SS BOND : bond 0.00389 / 0.26 ( 42) SS BOND : angle 1.34864 / 0.95 ( 84) hydrogen bonds : bond 0.02925 / 1.93 ( 606) hydrogen bonds : angle 4.32786 / 3.09 ( 1683) link_ALPHA1-3 : bond 0.01125 / 0.62 ( 6) link_ALPHA1-3 : angle 2.30500 / 1.36 ( 18) link_ALPHA1-6 : bond 0.00514 / 0.26 ( 3) link_ALPHA1-6 : angle 1.84140 / 1.01 ( 9) link_BETA1-4 : bond 0.00482 / 0.28 ( 12) link_BETA1-4 : angle 1.59969 / 1.04 ( 36) link_NAG-ASN : bond 0.00542 / 0.37 ( 54) link_NAG-ASN : angle 3.36216 / 2.31 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4623.67 seconds wall clock time: 80 minutes 2.62 seconds (4802.62 seconds total)