Starting phenix.real_space_refine on Fri Aug 7 06:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yie_72987/08_2026/9yie_72987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yie_72987/08_2026/9yie_72987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yie_72987/08_2026/9yie_72987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yie_72987/08_2026/9yie_72987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yie_72987/08_2026/9yie_72987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yie_72987/08_2026/9yie_72987.map" } resolution = 4.3 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= 0.007 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 12057 2.51 5 N 3252 2.21 5 O 3873 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: 19305 Number of models: 1 Model: "" Number of chains: 33 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: 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: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "J" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "N" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.41, per 1000 atoms: 0.23 Number of scatterers: 19305 At special positions: 0 Unit cell: (136.59, 142.68, 144.42, 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 3873 8.00 N 3252 7.00 C 12057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 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=2.04 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=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " 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 156 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 230 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 392 " " NAG E 610 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 197 " " NAG F 604 " - " ASN F 230 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 301 " " NAG F 609 " - " ASN F 392 " " NAG F 610 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 230 " " NAG G 605 " - " ASN G 234 " " NAG G 606 " - " ASN G 276 " " NAG G 607 " - " ASN G 295 " " NAG G 608 " - " ASN G 301 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 448 " " NAG I 1 " - " ASN E 160 " " NAG O 1 " - " ASN E 262 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN F 156 " " NAG S 1 " - " ASN F 160 " " NAG T 1 " - " ASN F 262 " " NAG U 1 " - " ASN F 332 " " NAG V 1 " - " ASN F 386 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 262 " " NAG Z 1 " - " ASN G 332 " " NAG a 1 " - " ASN G 386 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 823.3 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 42 sheets defined 19.0% 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: 4.097A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.617A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.534A pdb=" N TRP A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.839A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.771A 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: 4.098A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.617A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.534A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.839A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.771A 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: 4.097A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.617A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.535A pdb=" N TRP C 631 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.839A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.772A 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 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.619A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.589A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.523A 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: 4.045A 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 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.619A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.588A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.523A 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: 4.045A 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 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.619A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.589A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.524A 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: 4.046A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 4.073A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 64 removed outlier: 4.073A pdb=" N GLN J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 removed outlier: 4.074A pdb=" N GLN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.821A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.821A pdb=" N THR B 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL F 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.820A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.889A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AA7, first strand: chain 'E' and resid 157 through 162 Processing sheet with id=AA8, first strand: chain 'E' and resid 271 through 274 removed outlier: 7.320A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.613A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 301 through 308 removed outlier: 4.299A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.889A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AB6, first strand: chain 'F' and resid 157 through 162 Processing sheet with id=AB7, first strand: chain 'F' and resid 271 through 274 removed outlier: 7.319A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.613A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 308 removed outlier: 4.300A pdb=" N ASP F 321A" --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS F 305 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.890A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AC5, first strand: chain 'G' and resid 157 through 162 Processing sheet with id=AC6, first strand: chain 'G' and resid 271 through 274 removed outlier: 7.319A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.613A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 301 through 308 removed outlier: 4.299A pdb=" N ASP G 321A" --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.633A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.633A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 51 removed outlier: 5.633A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 45 through 51 removed outlier: 5.633A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.644A pdb=" N ALA K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 22 through 26 Processing sheet with id=AD9, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.645A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 22 through 26 Processing sheet with id=AE2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'M' and resid 45 through 51 removed outlier: 5.634A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 45 through 51 removed outlier: 5.634A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.643A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 22 through 26 639 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: 3.15 Time building geometry restraints manager: 2.10 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: 6135 1.34 - 1.46: 4433 1.46 - 1.58: 8965 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 19689 Sorted by residual: bond pdb=" C SER M 100D" pdb=" N PRO M 100E" ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.70e+00 bond pdb=" C SER H 100D" pdb=" N PRO H 100E" ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.67e+00 bond pdb=" C SER J 100D" pdb=" N PRO J 100E" ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 bond pdb=" C2 BMA O 3 " pdb=" O2 BMA O 3 " ideal model delta sigma weight residual 1.402 1.434 -0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C2 BMA T 3 " pdb=" O2 BMA T 3 " ideal model delta sigma weight residual 1.402 1.433 -0.031 2.00e-02 2.50e+03 2.48e+00 ... (remaining 19684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 26053 1.80 - 3.61: 632 3.61 - 5.41: 57 5.41 - 7.22: 12 7.22 - 9.02: 3 Bond angle restraints: 26757 Sorted by residual: angle pdb=" C1 BMA O 3 " pdb=" O5 BMA O 3 " pdb=" C5 BMA O 3 " ideal model delta sigma weight residual 118.82 109.80 9.02 3.00e+00 1.11e-01 9.04e+00 angle pdb=" C1 BMA Y 3 " pdb=" O5 BMA Y 3 " pdb=" C5 BMA Y 3 " ideal model delta sigma weight residual 118.82 109.82 9.00 3.00e+00 1.11e-01 9.00e+00 angle pdb=" C1 BMA T 3 " pdb=" O5 BMA T 3 " pdb=" C5 BMA T 3 " ideal model delta sigma weight residual 118.82 109.87 8.95 3.00e+00 1.11e-01 8.89e+00 angle pdb=" C LEU A 602 " pdb=" CA LEU A 602 " pdb=" CB LEU A 602 " ideal model delta sigma weight residual 110.42 115.91 -5.49 1.99e+00 2.53e-01 7.62e+00 angle pdb=" C LEU C 602 " pdb=" CA LEU C 602 " pdb=" CB LEU C 602 " ideal model delta sigma weight residual 110.42 115.91 -5.49 1.99e+00 2.53e-01 7.62e+00 ... (remaining 26752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 11755 24.23 - 48.46: 773 48.46 - 72.69: 108 72.69 - 96.92: 33 96.92 - 121.15: 36 Dihedral angle restraints: 12705 sinusoidal: 5919 harmonic: 6786 Sorted by residual: dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual 93.00 15.94 77.06 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual 93.00 15.97 77.03 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 16.00 77.00 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 12702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 3207 1.004 - 2.008: 0 2.008 - 3.012: 0 3.012 - 4.016: 0 4.016 - 5.020: 6 Chirality restraints: 3213 Sorted by residual: chirality pdb=" C4 NAG T 2 " pdb=" C3 NAG T 2 " pdb=" C5 NAG T 2 " pdb=" O4 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.53 2.49 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C4 NAG O 2 " pdb=" C3 NAG O 2 " pdb=" C5 NAG O 2 " pdb=" O4 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.53 2.49 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C4 NAG Y 2 " pdb=" C3 NAG Y 2 " pdb=" C5 NAG Y 2 " pdb=" O4 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.53 2.49 -5.02 2.00e-01 2.50e+01 6.29e+02 ... (remaining 3210 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 139 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C THR F 139 " -0.021 2.00e-02 2.50e+03 pdb=" O THR F 139 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN F 140 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 139 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C THR G 139 " -0.021 2.00e-02 2.50e+03 pdb=" O THR G 139 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN G 140 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 139 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C THR E 139 " -0.021 2.00e-02 2.50e+03 pdb=" O THR E 139 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN E 140 " 0.007 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 12684 3.07 - 3.53: 19084 3.53 - 3.98: 28850 3.98 - 4.44: 33714 4.44 - 4.90: 53168 Nonbonded interactions: 147500 Sorted by model distance: nonbonded pdb=" N ASP N 82 " pdb=" OD1 ASP N 82 " model vdw 2.610 3.120 nonbonded pdb=" N ASP L 82 " pdb=" OD1 ASP L 82 " model vdw 2.610 3.120 nonbonded pdb=" N ASP K 82 " pdb=" OD1 ASP K 82 " model vdw 2.611 3.120 nonbonded pdb=" N ASN G 137 " pdb=" O ASN G 137 " model vdw 2.618 2.496 nonbonded pdb=" N ASN F 137 " pdb=" O ASN F 137 " model vdw 2.618 2.496 ... (remaining 147495 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.640 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 0.038 19797 Z= 0.208 Angle : 0.672 17.928 27042 Z= 0.296 Chirality : 0.222 5.020 3213 Planarity : 0.003 0.029 3327 Dihedral : 17.146 121.149 8214 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.02 % Allowed : 10.50 % Favored : 88.49 % 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: -0.49 (0.18), residues: 2304 helix: 1.87 (0.28), residues: 411 sheet: 0.01 (0.22), residues: 582 loop : -1.24 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 94 TYR 0.009 0.001 TYR K 87 PHE 0.011 0.001 PHE M 78 TRP 0.009 0.001 TRP J 103 HIS 0.002 0.000 HIS F 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (19689) covalent geometry : angle 0.61464 / 0.28 (26757) SS BOND : bond 0.00408 / 0.23 ( 39) SS BOND : angle 0.61533 / 0.39 ( 78) hydrogen bonds : bond 0.07744 / 4.94 ( 594) hydrogen bonds : angle 6.09912 / 4.43 ( 1683) link_ALPHA1-3 : bond 0.00202 / 0.10 ( 3) link_ALPHA1-3 : angle 1.49120 / 0.74 ( 9) link_BETA1-4 : bond 0.01005 / 0.66 ( 18) link_BETA1-4 : angle 1.89509 / 1.24 ( 54) link_NAG-ASN : bond 0.00717 / 0.43 ( 48) link_NAG-ASN : angle 3.60090 / 2.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 472 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8143 (t) cc_final: 0.7729 (m) REVERT: A 658 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 659 ASP cc_start: 0.8891 (t70) cc_final: 0.8663 (t70) REVERT: B 529 THR cc_start: 0.8107 (t) cc_final: 0.7606 (m) REVERT: B 575 GLN cc_start: 0.8022 (pp30) cc_final: 0.7623 (tp40) REVERT: B 658 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8845 (tm-30) REVERT: B 659 ASP cc_start: 0.8899 (t70) cc_final: 0.8694 (t0) REVERT: C 529 THR cc_start: 0.8269 (t) cc_final: 0.7719 (m) REVERT: C 658 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8654 (tm-30) REVERT: E 95 MET cc_start: 0.7998 (ptm) cc_final: 0.7574 (ppp) REVERT: E 131 CYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7184 (m) REVERT: E 289 ASN cc_start: 0.8612 (p0) cc_final: 0.8267 (p0) REVERT: E 321 ASP cc_start: 0.7994 (t0) cc_final: 0.7395 (m-30) REVERT: E 377 ASN cc_start: 0.9239 (t0) cc_final: 0.8832 (t0) REVERT: E 434 MET cc_start: 0.8736 (tmm) cc_final: 0.8459 (tmm) REVERT: F 67 ASN cc_start: 0.8810 (t0) cc_final: 0.8497 (t0) REVERT: F 95 MET cc_start: 0.8090 (ptm) cc_final: 0.7691 (ppp) REVERT: F 131 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7334 (m) REVERT: F 142 MET cc_start: 0.7934 (tpp) cc_final: 0.7726 (tpp) REVERT: F 161 MET cc_start: 0.9113 (tpp) cc_final: 0.8195 (tpt) REVERT: F 321 ASP cc_start: 0.8028 (t0) cc_final: 0.7311 (m-30) REVERT: F 434 MET cc_start: 0.8940 (tmm) cc_final: 0.8713 (tmm) REVERT: F 486 TYR cc_start: 0.9202 (m-80) cc_final: 0.8933 (m-80) REVERT: G 45 TRP cc_start: 0.7940 (p90) cc_final: 0.7712 (p90) REVERT: G 95 MET cc_start: 0.7960 (ptm) cc_final: 0.7622 (ppp) REVERT: G 131 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7324 (m) REVERT: G 161 MET cc_start: 0.8942 (tpp) cc_final: 0.7846 (tpt) REVERT: G 256 SER cc_start: 0.9424 (p) cc_final: 0.8820 (m) REVERT: G 321 ASP cc_start: 0.7925 (t0) cc_final: 0.7209 (m-30) REVERT: G 372 THR cc_start: 0.9024 (p) cc_final: 0.8793 (p) REVERT: G 427 TRP cc_start: 0.8602 (m-10) cc_final: 0.8021 (m-90) REVERT: G 486 TYR cc_start: 0.9117 (m-80) cc_final: 0.8913 (m-80) REVERT: M 36 TRP cc_start: 0.8046 (m100) cc_final: 0.7824 (m100) outliers start: 21 outliers final: 6 residues processed: 485 average time/residue: 0.1325 time to fit residues: 96.5181 Evaluate side-chains 327 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 318 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.0040 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 95 GLN J 56 ASN J 60 ASN J 95 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN M 95 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098857 restraints weight = 35596.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099817 restraints weight = 29077.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100648 restraints weight = 23374.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101275 restraints weight = 18110.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101412 restraints weight = 16974.078| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19797 Z= 0.203 Angle : 0.735 18.388 27042 Z= 0.340 Chirality : 0.049 0.416 3213 Planarity : 0.004 0.066 3327 Dihedral : 6.997 55.936 3945 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % 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: -0.59 (0.18), residues: 2304 helix: 1.77 (0.28), residues: 405 sheet: -0.22 (0.22), residues: 588 loop : -1.20 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 542 TYR 0.014 0.002 TYR K 87 PHE 0.017 0.002 PHE G 233 TRP 0.016 0.002 TRP C 631 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (19689) covalent geometry : angle 0.66113 / 0.32 (26757) SS BOND : bond 0.00300 / 0.18 ( 39) SS BOND : angle 1.35073 / 0.93 ( 78) hydrogen bonds : bond 0.03405 / 2.25 ( 594) hydrogen bonds : angle 5.03470 / 3.65 ( 1683) link_ALPHA1-3 : bond 0.01521 / 0.76 ( 3) link_ALPHA1-3 : angle 2.43384 / 1.28 ( 9) link_BETA1-4 : bond 0.00517 / 0.30 ( 18) link_BETA1-4 : angle 3.10119 / 2.16 ( 54) link_NAG-ASN : bond 0.00713 / 0.43 ( 48) link_NAG-ASN : angle 3.92174 / 2.81 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 402 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8150 (t) cc_final: 0.7761 (m) REVERT: A 603 ILE cc_start: 0.9251 (mm) cc_final: 0.8986 (tp) REVERT: A 658 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8772 (tm-30) REVERT: A 659 ASP cc_start: 0.8909 (t70) cc_final: 0.8558 (t70) REVERT: B 529 THR cc_start: 0.8079 (t) cc_final: 0.7523 (m) REVERT: B 603 ILE cc_start: 0.9151 (mm) cc_final: 0.8823 (tp) REVERT: B 647 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7398 (tt0) REVERT: B 658 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8823 (tm-30) REVERT: C 529 THR cc_start: 0.8293 (t) cc_final: 0.7767 (m) REVERT: C 658 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8715 (tm-30) REVERT: E 95 MET cc_start: 0.8218 (ptm) cc_final: 0.7802 (ppp) REVERT: E 161 MET cc_start: 0.8781 (tpp) cc_final: 0.8329 (ttm) REVERT: E 202 THR cc_start: 0.9325 (p) cc_final: 0.9101 (t) REVERT: E 258 GLN cc_start: 0.9309 (mt0) cc_final: 0.9050 (mt0) REVERT: E 321 ASP cc_start: 0.8132 (t0) cc_final: 0.7435 (m-30) REVERT: E 372 THR cc_start: 0.9018 (p) cc_final: 0.8800 (p) REVERT: E 377 ASN cc_start: 0.9113 (t0) cc_final: 0.8803 (t0) REVERT: E 434 MET cc_start: 0.8791 (tmm) cc_final: 0.8209 (tmm) REVERT: F 95 MET cc_start: 0.8142 (ptm) cc_final: 0.7848 (ppp) REVERT: F 161 MET cc_start: 0.8988 (tpp) cc_final: 0.8447 (ttm) REVERT: F 321 ASP cc_start: 0.8306 (t0) cc_final: 0.7505 (m-30) REVERT: F 427 TRP cc_start: 0.8696 (m-10) cc_final: 0.8302 (m-90) REVERT: F 486 TYR cc_start: 0.9199 (m-80) cc_final: 0.8829 (m-80) REVERT: G 95 MET cc_start: 0.8133 (ptm) cc_final: 0.7752 (ppp) REVERT: G 104 MET cc_start: 0.9114 (ttm) cc_final: 0.8544 (tpp) REVERT: G 120 VAL cc_start: 0.9159 (t) cc_final: 0.8724 (t) REVERT: G 161 MET cc_start: 0.9005 (tpp) cc_final: 0.8328 (ttm) REVERT: G 180 ASP cc_start: 0.8242 (m-30) cc_final: 0.8019 (m-30) REVERT: G 202 THR cc_start: 0.9231 (p) cc_final: 0.8963 (t) REVERT: G 256 SER cc_start: 0.9442 (p) cc_final: 0.8756 (m) REVERT: G 258 GLN cc_start: 0.9359 (mt0) cc_final: 0.8996 (mt0) REVERT: G 321 ASP cc_start: 0.8172 (t0) cc_final: 0.7429 (m-30) REVERT: G 377 ASN cc_start: 0.9161 (t0) cc_final: 0.8905 (t0) REVERT: G 434 MET cc_start: 0.8820 (tmm) cc_final: 0.8370 (tmm) REVERT: H 13 LYS cc_start: 0.7352 (mmtt) cc_final: 0.7067 (mmtt) REVERT: H 36 TRP cc_start: 0.8234 (m100) cc_final: 0.7866 (m100) REVERT: H 60 ASN cc_start: 0.7086 (OUTLIER) cc_final: 0.6831 (t0) REVERT: H 89 VAL cc_start: 0.8801 (t) cc_final: 0.8564 (m) REVERT: J 77 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7850 (tp-100) REVERT: M 6 GLU cc_start: 0.7493 (pm20) cc_final: 0.7056 (pt0) REVERT: M 77 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7658 (tp-100) outliers start: 3 outliers final: 0 residues processed: 405 average time/residue: 0.1385 time to fit residues: 85.2573 Evaluate side-chains 318 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 96 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 159 optimal weight: 0.0970 chunk 98 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 656 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 46 GLN J 39 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102941 restraints weight = 35067.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103383 restraints weight = 31326.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104144 restraints weight = 29324.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104684 restraints weight = 21563.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104797 restraints weight = 19345.720| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19797 Z= 0.124 Angle : 0.627 17.854 27042 Z= 0.299 Chirality : 0.046 0.433 3213 Planarity : 0.003 0.071 3327 Dihedral : 6.398 46.364 3945 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2304 helix: 1.72 (0.28), residues: 396 sheet: -0.23 (0.22), residues: 585 loop : -1.18 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.013 0.001 TYR K 87 PHE 0.014 0.001 PHE H 78 TRP 0.018 0.001 TRP B 631 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (19689) covalent geometry : angle 0.56254 / 0.28 (26757) SS BOND : bond 0.00211 / 0.12 ( 39) SS BOND : angle 0.89962 / 0.61 ( 78) hydrogen bonds : bond 0.03172 / 2.10 ( 594) hydrogen bonds : angle 4.82292 / 3.47 ( 1683) link_ALPHA1-3 : bond 0.00724 / 0.36 ( 3) link_ALPHA1-3 : angle 1.51452 / 0.82 ( 9) link_BETA1-4 : bond 0.00340 / 0.20 ( 18) link_BETA1-4 : angle 2.04116 / 1.44 ( 54) link_NAG-ASN : bond 0.00711 / 0.42 ( 48) link_NAG-ASN : angle 3.60496 / 2.62 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8074 (t) cc_final: 0.7679 (m) REVERT: A 603 ILE cc_start: 0.9264 (mm) cc_final: 0.8952 (tp) REVERT: A 658 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8706 (tm-30) REVERT: A 659 ASP cc_start: 0.8941 (t70) cc_final: 0.8630 (t70) REVERT: B 529 THR cc_start: 0.7969 (t) cc_final: 0.7481 (m) REVERT: B 603 ILE cc_start: 0.9133 (mm) cc_final: 0.8817 (tp) REVERT: C 529 THR cc_start: 0.8045 (t) cc_final: 0.7585 (m) REVERT: C 655 LYS cc_start: 0.8479 (tppt) cc_final: 0.8222 (mmmt) REVERT: E 95 MET cc_start: 0.8154 (ptm) cc_final: 0.7657 (ppp) REVERT: E 161 MET cc_start: 0.8917 (tpp) cc_final: 0.8627 (tpt) REVERT: E 202 THR cc_start: 0.9281 (p) cc_final: 0.9044 (t) REVERT: E 256 SER cc_start: 0.9431 (p) cc_final: 0.9192 (p) REVERT: E 258 GLN cc_start: 0.9307 (mt0) cc_final: 0.9033 (mt0) REVERT: E 321 ASP cc_start: 0.8134 (t0) cc_final: 0.7417 (m-30) REVERT: E 377 ASN cc_start: 0.9077 (t0) cc_final: 0.8798 (t0) REVERT: E 427 TRP cc_start: 0.8582 (m-10) cc_final: 0.8244 (m-90) REVERT: E 434 MET cc_start: 0.8775 (tmm) cc_final: 0.8172 (tmm) REVERT: F 67 ASN cc_start: 0.8619 (t0) cc_final: 0.8417 (p0) REVERT: F 95 MET cc_start: 0.8131 (ptm) cc_final: 0.7706 (ppp) REVERT: F 121 LYS cc_start: 0.9136 (tptm) cc_final: 0.8906 (tppt) REVERT: F 161 MET cc_start: 0.8949 (tpp) cc_final: 0.8509 (ttm) REVERT: F 213 ILE cc_start: 0.9149 (mt) cc_final: 0.8753 (mm) REVERT: F 256 SER cc_start: 0.9370 (p) cc_final: 0.8706 (m) REVERT: F 321 ASP cc_start: 0.8189 (t0) cc_final: 0.7452 (m-30) REVERT: F 427 TRP cc_start: 0.8711 (m-10) cc_final: 0.8213 (m-90) REVERT: F 486 TYR cc_start: 0.9162 (m-80) cc_final: 0.8884 (m-80) REVERT: G 95 MET cc_start: 0.8087 (ptm) cc_final: 0.7528 (ppp) REVERT: G 120 VAL cc_start: 0.9104 (t) cc_final: 0.8648 (t) REVERT: G 180 ASP cc_start: 0.8169 (m-30) cc_final: 0.7945 (m-30) REVERT: G 202 THR cc_start: 0.9208 (p) cc_final: 0.8930 (t) REVERT: G 258 GLN cc_start: 0.9339 (mt0) cc_final: 0.8965 (mt0) REVERT: G 321 ASP cc_start: 0.8210 (t0) cc_final: 0.7682 (m-30) REVERT: G 377 ASN cc_start: 0.9143 (t0) cc_final: 0.8892 (t0) REVERT: G 434 MET cc_start: 0.8773 (tmm) cc_final: 0.8282 (tmm) REVERT: H 13 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6904 (mmtt) REVERT: H 34 TRP cc_start: 0.8067 (t-100) cc_final: 0.7646 (t-100) REVERT: J 56 ASN cc_start: 0.7236 (m-40) cc_final: 0.6655 (m-40) REVERT: M 6 GLU cc_start: 0.7522 (pm20) cc_final: 0.7034 (pt0) REVERT: M 39 GLN cc_start: 0.8148 (tp-100) cc_final: 0.7904 (tp-100) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.1426 time to fit residues: 88.5674 Evaluate side-chains 312 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 139 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 194 optimal weight: 50.0000 chunk 180 optimal weight: 2.9990 chunk 228 optimal weight: 30.0000 chunk 221 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** 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 = 0.3489 r_free = 0.3489 target = 0.120311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093377 restraints weight = 36980.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.092526 restraints weight = 32434.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093454 restraints weight = 31529.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093974 restraints weight = 24262.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094118 restraints weight = 22282.123| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19797 Z= 0.234 Angle : 0.734 18.354 27042 Z= 0.351 Chirality : 0.048 0.431 3213 Planarity : 0.004 0.059 3327 Dihedral : 6.309 44.045 3945 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2304 helix: 1.18 (0.27), residues: 408 sheet: -0.53 (0.21), residues: 582 loop : -1.25 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 542 TYR 0.026 0.002 TYR F 217 PHE 0.014 0.002 PHE G 353 TRP 0.044 0.002 TRP E 479 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (19689) covalent geometry : angle 0.66381 / 0.34 (26757) SS BOND : bond 0.00516 / 0.30 ( 39) SS BOND : angle 1.47172 / 1.03 ( 78) hydrogen bonds : bond 0.03662 / 2.40 ( 594) hydrogen bonds : angle 5.01903 / 3.59 ( 1683) link_ALPHA1-3 : bond 0.00836 / 0.42 ( 3) link_ALPHA1-3 : angle 1.48439 / 0.82 ( 9) link_BETA1-4 : bond 0.00348 / 0.21 ( 18) link_BETA1-4 : angle 2.12023 / 1.37 ( 54) link_NAG-ASN : bond 0.00794 / 0.49 ( 48) link_NAG-ASN : angle 4.04272 / 2.88 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8250 (t) cc_final: 0.7871 (m) REVERT: A 659 ASP cc_start: 0.9067 (t70) cc_final: 0.8813 (t70) REVERT: B 658 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8877 (tm-30) REVERT: E 95 MET cc_start: 0.8354 (ptm) cc_final: 0.7901 (ppp) REVERT: E 161 MET cc_start: 0.8729 (tpp) cc_final: 0.8393 (ttm) REVERT: E 202 THR cc_start: 0.9406 (p) cc_final: 0.9111 (t) REVERT: E 213 ILE cc_start: 0.9126 (mt) cc_final: 0.8629 (mm) REVERT: E 258 GLN cc_start: 0.9296 (mt0) cc_final: 0.8944 (mt0) REVERT: E 321 ASP cc_start: 0.8344 (t0) cc_final: 0.7899 (m-30) REVERT: E 377 ASN cc_start: 0.9024 (t0) cc_final: 0.8744 (t0) REVERT: F 95 MET cc_start: 0.8273 (ptm) cc_final: 0.7933 (ppp) REVERT: F 213 ILE cc_start: 0.9180 (mt) cc_final: 0.8792 (mm) REVERT: F 377 ASN cc_start: 0.9008 (t0) cc_final: 0.8644 (t0) REVERT: G 95 MET cc_start: 0.8310 (ptm) cc_final: 0.7984 (ppp) REVERT: G 135 THR cc_start: 0.8589 (m) cc_final: 0.8384 (m) REVERT: G 180 ASP cc_start: 0.8436 (m-30) cc_final: 0.8221 (m-30) REVERT: G 202 THR cc_start: 0.9365 (p) cc_final: 0.9033 (t) REVERT: G 213 ILE cc_start: 0.9109 (mt) cc_final: 0.8644 (mm) REVERT: G 258 GLN cc_start: 0.9306 (mt0) cc_final: 0.8924 (mt0) REVERT: G 321 ASP cc_start: 0.8325 (t0) cc_final: 0.7845 (m-30) REVERT: G 377 ASN cc_start: 0.9103 (t0) cc_final: 0.8854 (t0) REVERT: G 434 MET cc_start: 0.8779 (tmm) cc_final: 0.8281 (tmm) REVERT: H 13 LYS cc_start: 0.7285 (mmtt) cc_final: 0.7000 (mmtt) REVERT: H 39 GLN cc_start: 0.8282 (tp40) cc_final: 0.8024 (tp-100) REVERT: H 77 GLN cc_start: 0.8037 (tp40) cc_final: 0.7670 (tp-100) REVERT: K 61 ARG cc_start: 0.5821 (ptm160) cc_final: 0.5519 (ptm160) REVERT: M 39 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7975 (tp-100) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1523 time to fit residues: 89.1291 Evaluate side-chains 297 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 221 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 228 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN J 39 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097294 restraints weight = 36529.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097329 restraints weight = 33746.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098103 restraints weight = 32271.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098684 restraints weight = 23593.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098721 restraints weight = 21863.510| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19797 Z= 0.135 Angle : 0.659 18.021 27042 Z= 0.314 Chirality : 0.046 0.435 3213 Planarity : 0.003 0.047 3327 Dihedral : 5.769 40.564 3945 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 (0.18), residues: 2304 helix: 1.26 (0.27), residues: 408 sheet: -0.47 (0.21), residues: 621 loop : -1.19 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 542 TYR 0.021 0.002 TYR F 486 PHE 0.014 0.001 PHE J 102 TRP 0.017 0.002 TRP L 35 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (19689) covalent geometry : angle 0.58817 / 0.30 (26757) SS BOND : bond 0.00208 / 0.12 ( 39) SS BOND : angle 1.31782 / 0.89 ( 78) hydrogen bonds : bond 0.03277 / 2.17 ( 594) hydrogen bonds : angle 4.70782 / 3.37 ( 1683) link_ALPHA1-3 : bond 0.00908 / 0.45 ( 3) link_ALPHA1-3 : angle 1.48370 / 0.80 ( 9) link_BETA1-4 : bond 0.00277 / 0.16 ( 18) link_BETA1-4 : angle 1.85660 / 1.24 ( 54) link_NAG-ASN : bond 0.00690 / 0.41 ( 48) link_NAG-ASN : angle 3.87596 / 2.78 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8087 (t) cc_final: 0.7690 (m) REVERT: A 659 ASP cc_start: 0.9035 (t70) cc_final: 0.8817 (t70) REVERT: B 529 THR cc_start: 0.8140 (t) cc_final: 0.7736 (m) REVERT: C 529 THR cc_start: 0.8235 (t) cc_final: 0.7750 (m) REVERT: C 658 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8744 (tm-30) REVERT: E 45 TRP cc_start: 0.7964 (p90) cc_final: 0.7564 (p90) REVERT: E 95 MET cc_start: 0.8314 (ptm) cc_final: 0.8056 (ppp) REVERT: E 161 MET cc_start: 0.8752 (tpp) cc_final: 0.8481 (ttm) REVERT: E 202 THR cc_start: 0.9246 (p) cc_final: 0.8919 (t) REVERT: E 213 ILE cc_start: 0.8800 (mt) cc_final: 0.8596 (mt) REVERT: E 256 SER cc_start: 0.9471 (p) cc_final: 0.9209 (p) REVERT: E 258 GLN cc_start: 0.9279 (mt0) cc_final: 0.8924 (mt0) REVERT: E 321 ASP cc_start: 0.8221 (t0) cc_final: 0.7631 (m-30) REVERT: E 377 ASN cc_start: 0.9102 (t0) cc_final: 0.8842 (t0) REVERT: E 434 MET cc_start: 0.8718 (tmm) cc_final: 0.8193 (tmm) REVERT: F 95 MET cc_start: 0.8312 (ptm) cc_final: 0.8069 (ppp) REVERT: F 256 SER cc_start: 0.9424 (p) cc_final: 0.9161 (p) REVERT: F 377 ASN cc_start: 0.9031 (t0) cc_final: 0.8643 (t0) REVERT: G 67 ASN cc_start: 0.8911 (t0) cc_final: 0.8378 (t0) REVERT: G 121 LYS cc_start: 0.9095 (tptm) cc_final: 0.8815 (tppt) REVERT: G 142 MET cc_start: 0.7878 (tpp) cc_final: 0.7631 (tpt) REVERT: G 258 GLN cc_start: 0.9303 (mt0) cc_final: 0.8886 (mt0) REVERT: G 321 ASP cc_start: 0.8302 (t0) cc_final: 0.7779 (m-30) REVERT: G 377 ASN cc_start: 0.9179 (t0) cc_final: 0.8933 (t0) REVERT: G 434 MET cc_start: 0.8811 (tmm) cc_final: 0.8361 (tmm) REVERT: H 6 GLU cc_start: 0.7842 (pm20) cc_final: 0.7296 (pt0) REVERT: H 13 LYS cc_start: 0.7329 (mmtt) cc_final: 0.7001 (mmtt) REVERT: H 39 GLN cc_start: 0.8369 (tp40) cc_final: 0.8034 (tp-100) REVERT: H 101 ASP cc_start: 0.9090 (p0) cc_final: 0.8773 (p0) REVERT: L 83 GLU cc_start: 0.5366 (mm-30) cc_final: 0.5056 (mm-30) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1276 time to fit residues: 77.6021 Evaluate side-chains 306 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 228 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 60 optimal weight: 0.0980 chunk 109 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 206 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 230 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 656 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098684 restraints weight = 36224.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099096 restraints weight = 33213.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100023 restraints weight = 30034.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100406 restraints weight = 21953.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100642 restraints weight = 20256.849| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19797 Z= 0.117 Angle : 0.644 18.004 27042 Z= 0.309 Chirality : 0.046 0.436 3213 Planarity : 0.003 0.040 3327 Dihedral : 5.403 40.057 3945 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.05 % Allowed : 1.60 % Favored : 98.36 % 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: -0.70 (0.18), residues: 2304 helix: 1.46 (0.27), residues: 399 sheet: -0.30 (0.21), residues: 609 loop : -1.19 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 542 TYR 0.017 0.001 TYR F 486 PHE 0.021 0.001 PHE K 98 TRP 0.028 0.002 TRP H 36 HIS 0.008 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19689) covalent geometry : angle 0.57689 / 0.29 (26757) SS BOND : bond 0.00341 / 0.21 ( 39) SS BOND : angle 1.06543 / 0.72 ( 78) hydrogen bonds : bond 0.03136 / 2.07 ( 594) hydrogen bonds : angle 4.61085 / 3.30 ( 1683) link_ALPHA1-3 : bond 0.01063 / 0.53 ( 3) link_ALPHA1-3 : angle 1.65513 / 0.88 ( 9) link_BETA1-4 : bond 0.00313 / 0.18 ( 18) link_BETA1-4 : angle 1.76267 / 1.17 ( 54) link_NAG-ASN : bond 0.00683 / 0.40 ( 48) link_NAG-ASN : angle 3.76729 / 2.71 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8045 (t) cc_final: 0.7628 (m) REVERT: A 630 GLN cc_start: 0.8539 (pm20) cc_final: 0.8323 (pm20) REVERT: A 634 GLU cc_start: 0.7805 (mp0) cc_final: 0.7542 (mp0) REVERT: A 658 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8642 (tm-30) REVERT: A 659 ASP cc_start: 0.9028 (t70) cc_final: 0.8691 (t70) REVERT: B 529 THR cc_start: 0.8121 (t) cc_final: 0.7740 (m) REVERT: C 529 THR cc_start: 0.8220 (t) cc_final: 0.7775 (m) REVERT: C 658 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8739 (tm-30) REVERT: E 45 TRP cc_start: 0.7945 (p90) cc_final: 0.7597 (p90) REVERT: E 95 MET cc_start: 0.8305 (ptm) cc_final: 0.8059 (ppp) REVERT: E 120 VAL cc_start: 0.9115 (t) cc_final: 0.8597 (t) REVERT: E 161 MET cc_start: 0.8753 (tpp) cc_final: 0.8428 (ttm) REVERT: E 202 THR cc_start: 0.9180 (p) cc_final: 0.8879 (t) REVERT: E 256 SER cc_start: 0.9504 (p) cc_final: 0.9236 (p) REVERT: E 258 GLN cc_start: 0.9275 (mt0) cc_final: 0.8917 (mt0) REVERT: E 321 ASP cc_start: 0.8174 (t0) cc_final: 0.7619 (m-30) REVERT: E 377 ASN cc_start: 0.9091 (t0) cc_final: 0.8828 (t0) REVERT: E 434 MET cc_start: 0.8761 (tmm) cc_final: 0.8192 (tmm) REVERT: F 161 MET cc_start: 0.8938 (tpp) cc_final: 0.8501 (ttm) REVERT: F 256 SER cc_start: 0.9289 (p) cc_final: 0.9036 (p) REVERT: F 377 ASN cc_start: 0.9068 (t0) cc_final: 0.8703 (t0) REVERT: G 53 PHE cc_start: 0.7336 (m-10) cc_final: 0.7027 (m-10) REVERT: G 95 MET cc_start: 0.8538 (ppp) cc_final: 0.8083 (ppp) REVERT: G 121 LYS cc_start: 0.9056 (tptm) cc_final: 0.8791 (tppt) REVERT: G 256 SER cc_start: 0.9445 (p) cc_final: 0.9241 (p) REVERT: G 258 GLN cc_start: 0.9301 (mt0) cc_final: 0.8905 (mt0) REVERT: G 321 ASP cc_start: 0.8279 (t0) cc_final: 0.7762 (m-30) REVERT: G 377 ASN cc_start: 0.9159 (t0) cc_final: 0.8909 (t0) REVERT: H 6 GLU cc_start: 0.7744 (pm20) cc_final: 0.7267 (pt0) REVERT: H 38 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7907 (mtm110) REVERT: H 101 ASP cc_start: 0.9076 (p0) cc_final: 0.8744 (p0) REVERT: K 37 GLN cc_start: 0.8277 (pp30) cc_final: 0.8026 (pp30) REVERT: M 36 TRP cc_start: 0.8027 (m100) cc_final: 0.7570 (m100) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.1287 time to fit residues: 81.2506 Evaluate side-chains 319 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 225 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 656 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN G 66 HIS ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096066 restraints weight = 36851.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096418 restraints weight = 34425.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097320 restraints weight = 30794.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097713 restraints weight = 23487.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097923 restraints weight = 21708.868| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19797 Z= 0.177 Angle : 0.686 18.209 27042 Z= 0.329 Chirality : 0.047 0.435 3213 Planarity : 0.003 0.040 3327 Dihedral : 5.492 41.230 3945 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2304 helix: 1.44 (0.27), residues: 399 sheet: -0.33 (0.22), residues: 570 loop : -1.33 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 542 TYR 0.016 0.002 TYR G 217 PHE 0.011 0.002 PHE H 78 TRP 0.036 0.002 TRP A 631 HIS 0.011 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (19689) covalent geometry : angle 0.61320 / 0.31 (26757) SS BOND : bond 0.00386 / 0.23 ( 39) SS BOND : angle 1.48162 / 1.06 ( 78) hydrogen bonds : bond 0.03349 / 2.22 ( 594) hydrogen bonds : angle 4.70458 / 3.38 ( 1683) link_ALPHA1-3 : bond 0.00913 / 0.46 ( 3) link_ALPHA1-3 : angle 1.43013 / 0.79 ( 9) link_BETA1-4 : bond 0.00234 / 0.14 ( 18) link_BETA1-4 : angle 1.79816 / 1.19 ( 54) link_NAG-ASN : bond 0.00706 / 0.42 ( 48) link_NAG-ASN : angle 4.00796 / 2.85 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8084 (t) cc_final: 0.7672 (m) REVERT: A 631 TRP cc_start: 0.8271 (t-100) cc_final: 0.7860 (t-100) REVERT: A 634 GLU cc_start: 0.7819 (mp0) cc_final: 0.7601 (mp0) REVERT: A 647 GLU cc_start: 0.7601 (tp30) cc_final: 0.7298 (tp30) REVERT: A 658 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 659 ASP cc_start: 0.9037 (t70) cc_final: 0.8664 (t70) REVERT: B 529 THR cc_start: 0.8161 (t) cc_final: 0.7725 (m) REVERT: C 529 THR cc_start: 0.8264 (t) cc_final: 0.7847 (m) REVERT: C 603 ILE cc_start: 0.9367 (mm) cc_final: 0.9134 (mm) REVERT: C 658 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8777 (tm-30) REVERT: E 95 MET cc_start: 0.8360 (ptm) cc_final: 0.8068 (ppp) REVERT: E 104 MET cc_start: 0.9245 (ttm) cc_final: 0.8929 (ttm) REVERT: E 161 MET cc_start: 0.8857 (tpp) cc_final: 0.8500 (ttm) REVERT: E 202 THR cc_start: 0.9207 (p) cc_final: 0.8904 (t) REVERT: E 256 SER cc_start: 0.9469 (p) cc_final: 0.9199 (p) REVERT: E 258 GLN cc_start: 0.9232 (mt0) cc_final: 0.8804 (mt0) REVERT: E 321 ASP cc_start: 0.8313 (t0) cc_final: 0.7750 (m-30) REVERT: E 377 ASN cc_start: 0.9117 (t0) cc_final: 0.8867 (t0) REVERT: F 161 MET cc_start: 0.8990 (tpp) cc_final: 0.8574 (ttm) REVERT: F 256 SER cc_start: 0.9323 (p) cc_final: 0.9049 (p) REVERT: F 377 ASN cc_start: 0.9128 (t0) cc_final: 0.8788 (t0) REVERT: G 95 MET cc_start: 0.8558 (ppp) cc_final: 0.8347 (ppp) REVERT: G 121 LYS cc_start: 0.9065 (tptm) cc_final: 0.8781 (tppt) REVERT: G 180 ASP cc_start: 0.8609 (m-30) cc_final: 0.8391 (m-30) REVERT: G 256 SER cc_start: 0.9465 (p) cc_final: 0.9257 (p) REVERT: G 258 GLN cc_start: 0.9285 (mt0) cc_final: 0.8849 (mt0) REVERT: G 321 ASP cc_start: 0.8331 (t0) cc_final: 0.7807 (m-30) REVERT: G 421 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8784 (tttt) REVERT: H 6 GLU cc_start: 0.7880 (pm20) cc_final: 0.7280 (pt0) REVERT: H 38 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8012 (mtm110) REVERT: H 101 ASP cc_start: 0.9093 (p0) cc_final: 0.8784 (p0) REVERT: L 37 GLN cc_start: 0.8485 (pp30) cc_final: 0.8284 (pp30) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.1353 time to fit residues: 83.8334 Evaluate side-chains 313 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 118 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095420 restraints weight = 36514.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095598 restraints weight = 32175.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096516 restraints weight = 29601.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097286 restraints weight = 22801.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097513 restraints weight = 20580.353| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19797 Z= 0.160 Angle : 0.678 18.160 27042 Z= 0.327 Chirality : 0.047 0.436 3213 Planarity : 0.003 0.039 3327 Dihedral : 5.456 40.666 3945 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.90 (0.17), residues: 2304 helix: 1.37 (0.27), residues: 399 sheet: -0.40 (0.21), residues: 588 loop : -1.35 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 542 TYR 0.023 0.002 TYR L 87 PHE 0.013 0.001 PHE J 102 TRP 0.043 0.002 TRP H 36 HIS 0.008 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (19689) covalent geometry : angle 0.60615 / 0.31 (26757) SS BOND : bond 0.00392 / 0.18 ( 39) SS BOND : angle 1.39067 / 0.98 ( 78) hydrogen bonds : bond 0.03352 / 2.24 ( 594) hydrogen bonds : angle 4.69119 / 3.34 ( 1683) link_ALPHA1-3 : bond 0.00899 / 0.45 ( 3) link_ALPHA1-3 : angle 1.31609 / 0.73 ( 9) link_BETA1-4 : bond 0.00233 / 0.13 ( 18) link_BETA1-4 : angle 1.72917 / 1.15 ( 54) link_NAG-ASN : bond 0.00686 / 0.41 ( 48) link_NAG-ASN : angle 3.97881 / 2.83 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8190 (t) cc_final: 0.7763 (m) REVERT: A 591 GLN cc_start: 0.8742 (tt0) cc_final: 0.8516 (tt0) REVERT: A 595 ILE cc_start: 0.8739 (tp) cc_final: 0.8308 (tp) REVERT: A 647 GLU cc_start: 0.7546 (tp30) cc_final: 0.7313 (tp30) REVERT: A 658 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8667 (tm-30) REVERT: A 659 ASP cc_start: 0.9043 (t70) cc_final: 0.8686 (t70) REVERT: B 529 THR cc_start: 0.8243 (t) cc_final: 0.7827 (m) REVERT: C 529 THR cc_start: 0.8301 (t) cc_final: 0.7943 (m) REVERT: C 603 ILE cc_start: 0.9390 (mm) cc_final: 0.9115 (mm) REVERT: C 658 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8753 (tm-30) REVERT: E 95 MET cc_start: 0.8386 (ptm) cc_final: 0.8047 (ppp) REVERT: E 104 MET cc_start: 0.9359 (ttm) cc_final: 0.8737 (ttm) REVERT: E 161 MET cc_start: 0.8853 (tpp) cc_final: 0.8486 (ttm) REVERT: E 202 THR cc_start: 0.9240 (p) cc_final: 0.8934 (t) REVERT: E 256 SER cc_start: 0.9502 (p) cc_final: 0.9240 (p) REVERT: E 258 GLN cc_start: 0.9210 (mt0) cc_final: 0.8794 (mt0) REVERT: E 321 ASP cc_start: 0.8327 (t0) cc_final: 0.7779 (m-30) REVERT: E 377 ASN cc_start: 0.9134 (t0) cc_final: 0.8925 (t0) REVERT: F 95 MET cc_start: 0.8544 (ppp) cc_final: 0.8069 (ppp) REVERT: F 139 THR cc_start: 0.9197 (t) cc_final: 0.8980 (t) REVERT: F 161 MET cc_start: 0.8997 (tpp) cc_final: 0.8548 (ttm) REVERT: F 256 SER cc_start: 0.9345 (p) cc_final: 0.9031 (p) REVERT: F 377 ASN cc_start: 0.9124 (t0) cc_final: 0.8769 (t0) REVERT: G 95 MET cc_start: 0.8587 (ppp) cc_final: 0.8351 (ppp) REVERT: G 121 LYS cc_start: 0.9034 (tptm) cc_final: 0.8798 (tppt) REVERT: G 139 THR cc_start: 0.9188 (t) cc_final: 0.8956 (t) REVERT: G 180 ASP cc_start: 0.8610 (m-30) cc_final: 0.8408 (m-30) REVERT: G 258 GLN cc_start: 0.9285 (mt0) cc_final: 0.8856 (mt0) REVERT: G 321 ASP cc_start: 0.8364 (t0) cc_final: 0.7883 (m-30) REVERT: G 377 ASN cc_start: 0.8953 (t0) cc_final: 0.8603 (t0) REVERT: G 421 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8771 (tttt) REVERT: H 6 GLU cc_start: 0.7925 (pm20) cc_final: 0.7327 (pt0) REVERT: H 38 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8023 (mtm110) REVERT: H 101 ASP cc_start: 0.9109 (p0) cc_final: 0.8811 (p0) REVERT: J 56 ASN cc_start: 0.7459 (m-40) cc_final: 0.6725 (m-40) REVERT: J 101 ASP cc_start: 0.9041 (p0) cc_final: 0.8667 (p0) REVERT: J 102 PHE cc_start: 0.8242 (m-80) cc_final: 0.7970 (m-80) REVERT: M 63 LEU cc_start: 0.8232 (mm) cc_final: 0.8002 (mm) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1315 time to fit residues: 79.5905 Evaluate side-chains 309 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 226 optimal weight: 40.0000 chunk 75 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 651 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096073 restraints weight = 35774.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095625 restraints weight = 35920.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096484 restraints weight = 36043.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096889 restraints weight = 27411.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096968 restraints weight = 24910.871| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19797 Z= 0.190 Angle : 0.715 18.321 27042 Z= 0.348 Chirality : 0.047 0.440 3213 Planarity : 0.004 0.041 3327 Dihedral : 5.617 41.481 3945 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.99 (0.17), residues: 2304 helix: 1.22 (0.27), residues: 399 sheet: -0.48 (0.21), residues: 588 loop : -1.36 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 542 TYR 0.021 0.002 TYR G 217 PHE 0.012 0.002 PHE G 53 TRP 0.039 0.002 TRP A 631 HIS 0.008 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (19689) covalent geometry : angle 0.64404 / 0.33 (26757) SS BOND : bond 0.00305 / 0.18 ( 39) SS BOND : angle 1.44157 / 1.01 ( 78) hydrogen bonds : bond 0.03464 / 2.30 ( 594) hydrogen bonds : angle 4.78088 / 3.43 ( 1683) link_ALPHA1-3 : bond 0.00885 / 0.44 ( 3) link_ALPHA1-3 : angle 1.46090 / 0.82 ( 9) link_BETA1-4 : bond 0.00216 / 0.13 ( 18) link_BETA1-4 : angle 1.81844 / 1.19 ( 54) link_NAG-ASN : bond 0.00724 / 0.44 ( 48) link_NAG-ASN : angle 4.06134 / 2.89 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 ILE cc_start: 0.8773 (tp) cc_final: 0.8388 (tp) REVERT: A 640 GLN cc_start: 0.8176 (tp40) cc_final: 0.7893 (tp40) REVERT: A 659 ASP cc_start: 0.8988 (t70) cc_final: 0.8727 (t70) REVERT: B 543 ASN cc_start: 0.7193 (t0) cc_final: 0.6801 (t0) REVERT: B 658 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8830 (tm-30) REVERT: C 529 THR cc_start: 0.8252 (t) cc_final: 0.7856 (m) REVERT: C 603 ILE cc_start: 0.9372 (mm) cc_final: 0.9111 (mm) REVERT: C 647 GLU cc_start: 0.7975 (tt0) cc_final: 0.7661 (tt0) REVERT: E 95 MET cc_start: 0.8419 (ptm) cc_final: 0.8126 (ppp) REVERT: E 104 MET cc_start: 0.9002 (ttm) cc_final: 0.8742 (tpp) REVERT: E 202 THR cc_start: 0.9313 (p) cc_final: 0.9017 (t) REVERT: E 256 SER cc_start: 0.9410 (p) cc_final: 0.9158 (p) REVERT: E 258 GLN cc_start: 0.9207 (mt0) cc_final: 0.8809 (mt0) REVERT: E 377 ASN cc_start: 0.9030 (t0) cc_final: 0.8829 (t0) REVERT: F 95 MET cc_start: 0.8639 (ppp) cc_final: 0.8178 (ppp) REVERT: F 161 MET cc_start: 0.9022 (tpp) cc_final: 0.8572 (ttm) REVERT: F 202 THR cc_start: 0.9409 (p) cc_final: 0.9134 (t) REVERT: F 256 SER cc_start: 0.9224 (p) cc_final: 0.8903 (p) REVERT: F 377 ASN cc_start: 0.9060 (t0) cc_final: 0.8738 (t0) REVERT: G 95 MET cc_start: 0.8659 (ppp) cc_final: 0.8424 (ppp) REVERT: G 139 THR cc_start: 0.9048 (t) cc_final: 0.8672 (t) REVERT: G 180 ASP cc_start: 0.8448 (m-30) cc_final: 0.8207 (m-30) REVERT: G 258 GLN cc_start: 0.9294 (mt0) cc_final: 0.8843 (mt0) REVERT: G 377 ASN cc_start: 0.8924 (t0) cc_final: 0.8594 (t0) REVERT: H 6 GLU cc_start: 0.7927 (pm20) cc_final: 0.7299 (pt0) REVERT: H 101 ASP cc_start: 0.9063 (p0) cc_final: 0.8726 (p0) REVERT: J 100 SER cc_start: 0.8279 (m) cc_final: 0.7816 (p) REVERT: J 101 ASP cc_start: 0.9030 (p0) cc_final: 0.8705 (p0) REVERT: M 38 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8232 (tpp80) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1303 time to fit residues: 75.7007 Evaluate side-chains 297 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 241 ASN ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.121073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095832 restraints weight = 35799.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095411 restraints weight = 35689.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096505 restraints weight = 33109.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097047 restraints weight = 25018.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097205 restraints weight = 24395.858| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19797 Z= 0.186 Angle : 0.728 18.255 27042 Z= 0.355 Chirality : 0.047 0.444 3213 Planarity : 0.004 0.048 3327 Dihedral : 5.723 41.841 3945 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % 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: -0.99 (0.17), residues: 2304 helix: 1.11 (0.27), residues: 402 sheet: -0.52 (0.21), residues: 582 loop : -1.30 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 542 TYR 0.023 0.002 TYR G 217 PHE 0.016 0.002 PHE N 98 TRP 0.033 0.002 TRP N 35 HIS 0.010 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (19689) covalent geometry : angle 0.65764 / 0.34 (26757) SS BOND : bond 0.00435 / 0.30 ( 39) SS BOND : angle 1.54591 / 1.05 ( 78) hydrogen bonds : bond 0.03506 / 2.35 ( 594) hydrogen bonds : angle 4.82481 / 3.46 ( 1683) link_ALPHA1-3 : bond 0.00734 / 0.37 ( 3) link_ALPHA1-3 : angle 1.43070 / 0.80 ( 9) link_BETA1-4 : bond 0.00227 / 0.13 ( 18) link_BETA1-4 : angle 1.78421 / 1.17 ( 54) link_NAG-ASN : bond 0.00713 / 0.43 ( 48) link_NAG-ASN : angle 4.06931 / 2.89 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 THR cc_start: 0.8170 (t) cc_final: 0.7781 (m) REVERT: A 595 ILE cc_start: 0.8756 (tp) cc_final: 0.8447 (tp) REVERT: A 634 GLU cc_start: 0.7918 (mp0) cc_final: 0.7377 (mp0) REVERT: A 640 GLN cc_start: 0.8138 (tp40) cc_final: 0.7909 (tp40) REVERT: A 659 ASP cc_start: 0.8998 (t70) cc_final: 0.8716 (t70) REVERT: B 543 ASN cc_start: 0.7237 (t0) cc_final: 0.6903 (t0) REVERT: C 529 THR cc_start: 0.8207 (t) cc_final: 0.7824 (m) REVERT: C 603 ILE cc_start: 0.9372 (mm) cc_final: 0.9095 (mm) REVERT: E 95 MET cc_start: 0.8428 (ptm) cc_final: 0.8136 (ppp) REVERT: E 202 THR cc_start: 0.9280 (p) cc_final: 0.8973 (t) REVERT: E 256 SER cc_start: 0.9477 (p) cc_final: 0.9225 (p) REVERT: E 258 GLN cc_start: 0.9213 (mt0) cc_final: 0.8818 (mt0) REVERT: E 377 ASN cc_start: 0.9110 (t0) cc_final: 0.8907 (t0) REVERT: F 95 MET cc_start: 0.8635 (ppp) cc_final: 0.8159 (ppp) REVERT: F 161 MET cc_start: 0.9009 (tpp) cc_final: 0.8581 (ttm) REVERT: F 202 THR cc_start: 0.9408 (p) cc_final: 0.9135 (t) REVERT: F 256 SER cc_start: 0.9231 (p) cc_final: 0.8931 (p) REVERT: F 377 ASN cc_start: 0.9069 (t0) cc_final: 0.8751 (t0) REVERT: G 95 MET cc_start: 0.8654 (ppp) cc_final: 0.8416 (ppp) REVERT: G 139 THR cc_start: 0.9068 (t) cc_final: 0.8750 (t) REVERT: G 180 ASP cc_start: 0.8428 (m-30) cc_final: 0.8196 (m-30) REVERT: G 207 LYS cc_start: 0.6008 (tmtt) cc_final: 0.5778 (tmtt) REVERT: G 258 GLN cc_start: 0.9286 (mt0) cc_final: 0.8873 (mt0) REVERT: G 377 ASN cc_start: 0.8882 (t0) cc_final: 0.8562 (t0) REVERT: H 6 GLU cc_start: 0.7912 (pm20) cc_final: 0.7408 (pt0) REVERT: H 101 ASP cc_start: 0.9061 (p0) cc_final: 0.8732 (p0) REVERT: J 101 ASP cc_start: 0.9069 (p0) cc_final: 0.8731 (p0) REVERT: L 37 GLN cc_start: 0.8347 (pp30) cc_final: 0.8082 (pp30) REVERT: M 38 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8267 (tpp80) REVERT: M 101 ASP cc_start: 0.9257 (p0) cc_final: 0.8530 (p0) outliers start: 2 outliers final: 0 residues processed: 366 average time/residue: 0.1327 time to fit residues: 75.4798 Evaluate side-chains 293 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 189 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 241 ASN ** G 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093432 restraints weight = 36750.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094326 restraints weight = 28897.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095174 restraints weight = 24249.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095797 restraints weight = 18715.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095940 restraints weight = 17247.999| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19797 Z= 0.170 Angle : 0.717 18.194 27042 Z= 0.349 Chirality : 0.047 0.444 3213 Planarity : 0.004 0.048 3327 Dihedral : 5.675 41.883 3945 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.33 % Favored : 91.62 % Rotamer: Outliers : 0.15 % Allowed : 0.34 % Favored : 99.52 % 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: -0.98 (0.17), residues: 2304 helix: 1.10 (0.27), residues: 402 sheet: -0.47 (0.22), residues: 588 loop : -1.32 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 542 TYR 0.022 0.002 TYR G 217 PHE 0.013 0.002 PHE G 53 TRP 0.052 0.002 TRP H 36 HIS 0.010 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (19689) covalent geometry : angle 0.64503 / 0.33 (26757) SS BOND : bond 0.00328 / 0.20 ( 39) SS BOND : angle 1.68384 / 1.19 ( 78) hydrogen bonds : bond 0.03397 / 2.28 ( 594) hydrogen bonds : angle 4.76120 / 3.41 ( 1683) link_ALPHA1-3 : bond 0.00685 / 0.35 ( 3) link_ALPHA1-3 : angle 1.44836 / 0.81 ( 9) link_BETA1-4 : bond 0.00214 / 0.11 ( 18) link_BETA1-4 : angle 1.76069 / 1.15 ( 54) link_NAG-ASN : bond 0.00714 / 0.44 ( 48) link_NAG-ASN : angle 4.05638 / 2.88 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2828.41 seconds wall clock time: 49 minutes 58.22 seconds (2998.22 seconds total)