Starting phenix.real_space_refine on Fri Aug 7 08:19:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yif_72988/08_2026/9yif_72988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yif_72988/08_2026/9yif_72988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yif_72988/08_2026/9yif_72988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yif_72988/08_2026/9yif_72988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yif_72988/08_2026/9yif_72988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yif_72988/08_2026/9yif_72988.map" } resolution = 3.8 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= 0.013 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 129 5.16 5 C 12462 2.51 5 N 3342 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 19923 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} 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: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "J" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "K" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} 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: "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: "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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "G" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 4.70, per 1000 atoms: 0.24 Number of scatterers: 19923 At special positions: 0 Unit cell: (162.69, 171.39, 138.33, 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 129 16.00 O 3990 8.00 N 3342 7.00 C 12462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN O 8 " - " MAN O 9 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN W 8 " - " MAN W 9 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 10 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 10 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " MAN W 7 " - " MAN W 10 " ALPHA1-6 " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 8 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA W 3 " - " MAN W 7 " " MAN W 7 " - " MAN W 8 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN E 262 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 230 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 241 " " NAG E 609 " - " ASN E 276 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 344 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 230 " " NAG F 607 " - " ASN F 234 " " NAG F 608 " - " ASN F 241 " " NAG F 609 " - " ASN F 276 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 344 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 160 " " NAG G 605 " - " ASN G 197 " " NAG G 606 " - " ASN G 230 " " NAG G 607 " - " ASN G 234 " " NAG G 608 " - " ASN G 241 " " NAG G 609 " - " ASN G 276 " " NAG G 610 " - " ASN G 301 " " NAG G 611 " - " ASN G 344 " " NAG G 612 " - " ASN G 392 " " NAG G 613 " - " ASN G 448 " " NAG I 1 " - " ASN E 295 " " NAG O 1 " - " ASN E 332 " " NAG P 1 " - " ASN E 386 " " NAG Q 1 " - " ASN F 262 " " NAG R 1 " - " ASN F 295 " " NAG S 1 " - " ASN F 332 " " NAG T 1 " - " ASN F 386 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 295 " " NAG W 1 " - " ASN G 332 " " NAG X 1 " - " ASN G 386 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 710.7 milliseconds 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 20.5% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.633A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.182A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.511A 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 Processing helix chain 'A' and resid 638 through 651 removed outlier: 3.959A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 663 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.633A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.181A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.511A 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 Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.960A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 663 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.632A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 4.181A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.511A 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 Processing helix chain 'C' and resid 638 through 651 removed outlier: 3.959A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 663 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.511A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) 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 195 through 198 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.569A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.712A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.186A 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 122 through 126 removed outlier: 3.510A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (cutoff:3.500A) 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 195 through 198 Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.570A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.712A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.185A 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 122 through 126 removed outlier: 3.510A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) 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 195 through 198 Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.570A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.713A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.185A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 609 removed outlier: 3.693A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 604 through 609 removed outlier: 3.693A pdb=" N THR B 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL F 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 604 through 609 removed outlier: 3.693A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.836A 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: 3.741A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.899A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AA7, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'E' and resid 157 through 162 Processing sheet with id=AA9, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.470A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.755A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 302 through 308 removed outlier: 5.268A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.741A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 53 through 55 removed outlier: 3.898A pdb=" N PHE F 53 " --> pdb=" O CYS F 218 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS F 218 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AB7, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AB8, first strand: chain 'F' and resid 157 through 162 Processing sheet with id=AB9, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.470A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.755A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.268A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.741A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 53 through 55 removed outlier: 3.898A pdb=" N PHE G 53 " --> pdb=" O CYS G 218 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS G 218 " --> pdb=" O PHE G 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'G' and resid 157 through 162 Processing sheet with id=AC9, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.470A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.756A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 302 through 308 removed outlier: 5.268A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.507A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.741A pdb=" N GLY H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.741A pdb=" N GLY H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.507A pdb=" N VAL J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 18 " --> pdb=" O MET J 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.741A pdb=" N GLY J 10 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET J 34 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.741A pdb=" N GLY J 10 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AE2, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.003A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.003A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.507A pdb=" N VAL M 5 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU M 18 " --> pdb=" O MET M 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET M 82 " --> pdb=" O LEU M 18 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.741A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.741A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AE9, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.003A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1746 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: 3.05 Time building geometry restraints manager: 2.57 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: 6275 1.34 - 1.46: 4193 1.46 - 1.58: 9683 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 20325 Sorted by residual: bond pdb=" C THR G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.335 1.352 -0.017 9.40e-03 1.13e+04 3.38e+00 bond pdb=" C THR F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.335 1.352 -0.017 9.40e-03 1.13e+04 3.28e+00 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.335 1.352 -0.017 9.40e-03 1.13e+04 3.21e+00 bond pdb=" C2 MAN O 5 " pdb=" O2 MAN O 5 " ideal model delta sigma weight residual 1.407 1.443 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C2 MAN W 5 " pdb=" O2 MAN W 5 " ideal model delta sigma weight residual 1.407 1.442 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 20320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 27053 2.37 - 4.75: 467 4.75 - 7.12: 43 7.12 - 9.49: 7 9.49 - 11.86: 3 Bond angle restraints: 27573 Sorted by residual: angle pdb=" C1 MAN S 5 " pdb=" C2 MAN S 5 " pdb=" O2 MAN S 5 " ideal model delta sigma weight residual 106.80 118.66 -11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C1 MAN W 5 " pdb=" C2 MAN W 5 " pdb=" O2 MAN W 5 " ideal model delta sigma weight residual 106.80 118.61 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C1 MAN O 5 " pdb=" C2 MAN O 5 " pdb=" O2 MAN O 5 " ideal model delta sigma weight residual 106.80 118.57 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 109.82 9.00 3.00e+00 1.11e-01 8.99e+00 angle pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 118.82 109.83 8.99 3.00e+00 1.11e-01 8.97e+00 ... (remaining 27568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.26: 12623 24.26 - 48.51: 661 48.51 - 72.77: 36 72.77 - 97.03: 45 97.03 - 121.28: 60 Dihedral angle restraints: 13425 sinusoidal: 6606 harmonic: 6819 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.03 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.03 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.02 -58.02 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 13422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.019: 3321 1.019 - 2.037: 3 2.037 - 3.056: 0 3.056 - 4.075: 0 4.075 - 5.094: 9 Chirality restraints: 3333 Sorted by residual: chirality pdb=" C4 NAG E 604 " pdb=" C3 NAG E 604 " pdb=" C5 NAG E 604 " pdb=" O4 NAG E 604 " both_signs ideal model delta sigma weight residual False -2.53 2.56 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C4 NAG F 604 " pdb=" C3 NAG F 604 " pdb=" C5 NAG F 604 " pdb=" O4 NAG F 604 " both_signs ideal model delta sigma weight residual False -2.53 2.56 -5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C4 NAG G 604 " pdb=" C3 NAG G 604 " pdb=" C5 NAG G 604 " pdb=" O4 NAG G 604 " both_signs ideal model delta sigma weight residual False -2.53 2.56 -5.09 2.00e-01 2.50e+01 6.47e+02 ... (remaining 3330 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 7 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO K 8 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO K 8 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 8 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO L 8 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 7 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO N 8 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " 0.027 5.00e-02 4.00e+02 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 12321 3.05 - 3.51: 18418 3.51 - 3.98: 29982 3.98 - 4.44: 34513 4.44 - 4.90: 55826 Nonbonded interactions: 151060 Sorted by model distance: nonbonded pdb=" O ASN G 156 " pdb=" OD1 ASN G 156 " model vdw 2.589 3.040 nonbonded pdb=" O ASN E 156 " pdb=" OD1 ASN E 156 " model vdw 2.589 3.040 nonbonded pdb=" O ASN F 156 " pdb=" OD1 ASN F 156 " model vdw 2.589 3.040 nonbonded pdb=" O2 BMA S 3 " pdb=" O3 BMA S 3 " model vdw 2.629 2.432 nonbonded pdb=" O2 BMA O 3 " pdb=" O3 BMA O 3 " model vdw 2.630 2.432 ... (remaining 151055 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 'Q' selection = chain 'U' } 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 'I' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.860 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.005 0.036 20463 Z= 0.224 Angle : 0.680 11.864 27945 Z= 0.287 Chirality : 0.268 5.094 3333 Planarity : 0.003 0.048 3402 Dihedral : 16.518 121.285 8907 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2319 helix: 2.09 (0.28), residues: 390 sheet: 0.17 (0.20), residues: 669 loop : -1.11 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 71 TYR 0.006 0.001 TYR N 49 PHE 0.008 0.001 PHE F 159 TRP 0.004 0.001 TRP F 479 HIS 0.003 0.000 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (20325) covalent geometry : angle 0.64786 / 0.28 (27573) SS BOND : bond 0.00172 / 0.12 ( 42) SS BOND : angle 0.40998 / 0.28 ( 84) hydrogen bonds : bond 0.12652 / 8.26 ( 657) hydrogen bonds : angle 6.09799 / 4.32 ( 1746) link_ALPHA1-2 : bond 0.00177 / 0.09 ( 9) link_ALPHA1-2 : angle 2.15397 / 1.60 ( 27) link_ALPHA1-3 : bond 0.00140 / 0.09 ( 9) link_ALPHA1-3 : angle 1.17001 / 0.75 ( 27) link_ALPHA1-6 : bond 0.00236 / 0.14 ( 6) link_ALPHA1-6 : angle 0.99793 / 0.74 ( 18) link_BETA1-4 : bond 0.01091 / 0.61 ( 18) link_BETA1-4 : angle 2.02929 / 1.51 ( 54) link_NAG-ASN : bond 0.00351 / 0.23 ( 54) link_NAG-ASN : angle 2.39469 / 1.63 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 477 time to evaluate : 0.759 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: C 543 ASN cc_start: 0.8449 (m110) cc_final: 0.8232 (m110) REVERT: C 635 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7813 (mt) REVERT: E 125 LEU cc_start: 0.8826 (tp) cc_final: 0.8543 (tp) REVERT: E 161 MET cc_start: 0.8452 (tpp) cc_final: 0.7544 (tpt) REVERT: E 232 THR cc_start: 0.8196 (m) cc_final: 0.7796 (p) REVERT: E 365 SER cc_start: 0.8789 (p) cc_final: 0.8481 (t) REVERT: F 35 TRP cc_start: 0.8587 (m100) cc_final: 0.8128 (m-10) REVERT: F 232 THR cc_start: 0.8217 (m) cc_final: 0.7960 (p) REVERT: F 365 SER cc_start: 0.8801 (p) cc_final: 0.8509 (t) REVERT: F 442 VAL cc_start: 0.9460 (t) cc_final: 0.9240 (p) REVERT: G 35 TRP cc_start: 0.8456 (m100) cc_final: 0.8182 (m-10) REVERT: G 161 MET cc_start: 0.8412 (tpp) cc_final: 0.8147 (tpt) REVERT: G 232 THR cc_start: 0.8113 (m) cc_final: 0.7838 (p) REVERT: G 365 SER cc_start: 0.8857 (p) cc_final: 0.8583 (t) REVERT: G 442 VAL cc_start: 0.9447 (t) cc_final: 0.9209 (p) REVERT: H 100 TYR cc_start: 0.8890 (m-80) cc_final: 0.8665 (m-10) REVERT: H 100 LEU cc_start: 0.8677 (mt) cc_final: 0.8420 (mt) REVERT: J 52 SER cc_start: 0.8452 (p) cc_final: 0.8243 (m) REVERT: J 100 LEU cc_start: 0.8644 (mt) cc_final: 0.8366 (mt) REVERT: K 26 SER cc_start: 0.8960 (m) cc_final: 0.8706 (m) REVERT: L 26 SER cc_start: 0.8988 (m) cc_final: 0.8663 (m) REVERT: L 89 GLN cc_start: 0.8621 (tt0) cc_final: 0.8401 (tt0) REVERT: M 62 SER cc_start: 0.8248 (p) cc_final: 0.7902 (t) REVERT: N 26 SER cc_start: 0.9097 (m) cc_final: 0.8743 (m) outliers start: 3 outliers final: 0 residues processed: 480 average time/residue: 0.1560 time to fit residues: 114.5213 Evaluate side-chains 341 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 340 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 200 optimal weight: 8.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN A 630 GLN A 650 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 650 GLN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN C 650 GLN E 103 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN E 425 ASN F 103 GLN F 425 ASN G 103 GLN G 425 ASN K 27 GLN L 27 GLN N 27 GLN N 76 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126163 restraints weight = 25913.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129907 restraints weight = 15812.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132451 restraints weight = 11305.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134187 restraints weight = 8959.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135328 restraints weight = 7593.278| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20463 Z= 0.121 Angle : 0.687 17.994 27945 Z= 0.304 Chirality : 0.048 0.382 3333 Planarity : 0.003 0.039 3402 Dihedral : 9.318 79.508 4508 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.84 % Allowed : 13.69 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2319 helix: 1.98 (0.28), residues: 396 sheet: 0.26 (0.21), residues: 672 loop : -1.11 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 617 TYR 0.010 0.001 TYR K 49 PHE 0.020 0.002 PHE N 71 TRP 0.008 0.001 TRP N 35 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (20325) covalent geometry : angle 0.59087 / 0.28 (27573) SS BOND : bond 0.00196 / 0.14 ( 42) SS BOND : angle 0.62761 / 0.44 ( 84) hydrogen bonds : bond 0.03079 / 1.99 ( 657) hydrogen bonds : angle 4.90580 / 3.49 ( 1746) link_ALPHA1-2 : bond 0.00474 / 0.26 ( 9) link_ALPHA1-2 : angle 3.23465 / 2.32 ( 27) link_ALPHA1-3 : bond 0.01051 / 0.52 ( 9) link_ALPHA1-3 : angle 1.58762 / 1.00 ( 27) link_ALPHA1-6 : bond 0.00224 / 0.12 ( 6) link_ALPHA1-6 : angle 1.65704 / 1.06 ( 18) link_BETA1-4 : bond 0.00534 / 0.25 ( 18) link_BETA1-4 : angle 5.59166 / 4.48 ( 54) link_NAG-ASN : bond 0.00364 / 0.23 ( 54) link_NAG-ASN : angle 2.98581 / 2.04 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 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: 38 poor density : 358 time to evaluate : 0.746 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: B 651 ASN cc_start: 0.7465 (m-40) cc_final: 0.7129 (m-40) REVERT: E 35 TRP cc_start: 0.8470 (m100) cc_final: 0.8231 (m-10) REVERT: E 161 MET cc_start: 0.8378 (tpp) cc_final: 0.7600 (tpt) REVERT: E 232 THR cc_start: 0.8329 (m) cc_final: 0.8057 (p) REVERT: F 35 TRP cc_start: 0.8664 (m100) cc_final: 0.8020 (m-10) REVERT: F 365 SER cc_start: 0.8810 (p) cc_final: 0.8534 (t) REVERT: F 442 VAL cc_start: 0.9377 (t) cc_final: 0.9168 (p) REVERT: G 35 TRP cc_start: 0.8577 (m100) cc_final: 0.7990 (m-10) REVERT: G 97 LYS cc_start: 0.8813 (tppt) cc_final: 0.8501 (mmtp) REVERT: G 161 MET cc_start: 0.8324 (tpp) cc_final: 0.8071 (tpt) REVERT: G 178 ARG cc_start: 0.7966 (tpt90) cc_final: 0.7699 (tpt90) REVERT: G 232 THR cc_start: 0.8407 (m) cc_final: 0.8154 (p) REVERT: G 365 SER cc_start: 0.8885 (p) cc_final: 0.8617 (t) REVERT: J 100 LEU cc_start: 0.8888 (mt) cc_final: 0.8640 (mt) REVERT: K 26 SER cc_start: 0.8925 (m) cc_final: 0.8677 (m) REVERT: K 67 SER cc_start: 0.7817 (t) cc_final: 0.7580 (t) REVERT: L 26 SER cc_start: 0.8926 (m) cc_final: 0.8666 (m) REVERT: L 89 GLN cc_start: 0.8559 (tt0) cc_final: 0.8298 (tt0) REVERT: N 26 SER cc_start: 0.8945 (m) cc_final: 0.8662 (m) REVERT: N 31 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7517 (mmt-90) outliers start: 38 outliers final: 23 residues processed: 381 average time/residue: 0.1307 time to fit residues: 80.3108 Evaluate side-chains 355 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 332 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 352 HIS Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 352 HIS Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 178 optimal weight: 0.0030 chunk 15 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 195 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 176 optimal weight: 0.0770 overall best weight: 1.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN F 348 GLN G 246 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN K 27 GLN L 27 GLN L 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122035 restraints weight = 26273.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125699 restraints weight = 16033.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128176 restraints weight = 11524.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129869 restraints weight = 9179.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131052 restraints weight = 7810.006| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20463 Z= 0.161 Angle : 0.668 12.964 27945 Z= 0.304 Chirality : 0.049 0.454 3333 Planarity : 0.003 0.037 3402 Dihedral : 8.646 75.836 4506 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.42 % Allowed : 15.53 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2319 helix: 1.81 (0.28), residues: 396 sheet: 0.11 (0.20), residues: 678 loop : -1.21 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 504 TYR 0.013 0.001 TYR H 100A PHE 0.032 0.002 PHE N 83 TRP 0.009 0.001 TRP F 45 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (20325) covalent geometry : angle 0.58248 / 0.28 (27573) SS BOND : bond 0.00245 / 0.17 ( 42) SS BOND : angle 0.62570 / 0.41 ( 84) hydrogen bonds : bond 0.03226 / 2.10 ( 657) hydrogen bonds : angle 4.78491 / 3.41 ( 1746) link_ALPHA1-2 : bond 0.00439 / 0.25 ( 9) link_ALPHA1-2 : angle 3.34680 / 2.41 ( 27) link_ALPHA1-3 : bond 0.00707 / 0.36 ( 9) link_ALPHA1-3 : angle 1.40233 / 0.87 ( 27) link_ALPHA1-6 : bond 0.00232 / 0.13 ( 6) link_ALPHA1-6 : angle 1.68015 / 1.06 ( 18) link_BETA1-4 : bond 0.00673 / 0.42 ( 18) link_BETA1-4 : angle 1.92713 / 1.28 ( 54) link_NAG-ASN : bond 0.00512 / 0.34 ( 54) link_NAG-ASN : angle 3.91909 / 2.62 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 0.723 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: E 46 LYS cc_start: 0.8254 (mptt) cc_final: 0.8022 (mmtm) REVERT: E 161 MET cc_start: 0.8494 (tpp) cc_final: 0.7518 (tpt) REVERT: E 365 SER cc_start: 0.8810 (p) cc_final: 0.8556 (t) REVERT: F 35 TRP cc_start: 0.8741 (m100) cc_final: 0.8338 (m100) REVERT: F 114 GLN cc_start: 0.8138 (tt0) cc_final: 0.7875 (tt0) REVERT: F 289 ASN cc_start: 0.8204 (p0) cc_final: 0.7988 (p0) REVERT: F 365 SER cc_start: 0.8816 (p) cc_final: 0.8562 (t) REVERT: G 97 LYS cc_start: 0.8887 (tppt) cc_final: 0.8647 (mmtp) REVERT: G 161 MET cc_start: 0.8466 (tpp) cc_final: 0.8160 (tpt) REVERT: G 178 ARG cc_start: 0.7998 (tpt90) cc_final: 0.7768 (tpt90) REVERT: G 180 ASP cc_start: 0.8963 (m-30) cc_final: 0.8564 (t0) REVERT: G 365 SER cc_start: 0.8890 (p) cc_final: 0.8640 (t) REVERT: G 486 TYR cc_start: 0.9053 (m-80) cc_final: 0.8567 (m-10) REVERT: J 100 LEU cc_start: 0.8917 (mt) cc_final: 0.8691 (mt) REVERT: L 26 SER cc_start: 0.8864 (m) cc_final: 0.8597 (m) REVERT: N 26 SER cc_start: 0.8907 (m) cc_final: 0.8620 (m) outliers start: 50 outliers final: 29 residues processed: 356 average time/residue: 0.1358 time to fit residues: 77.1659 Evaluate side-chains 332 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 303 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 171 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 215 optimal weight: 0.0770 chunk 26 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 184 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122459 restraints weight = 26127.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126150 restraints weight = 15910.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128616 restraints weight = 11432.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130334 restraints weight = 9111.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131414 restraints weight = 7750.895| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20463 Z= 0.126 Angle : 0.641 12.759 27945 Z= 0.295 Chirality : 0.048 0.439 3333 Planarity : 0.003 0.036 3402 Dihedral : 7.957 69.468 4506 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.32 % Allowed : 17.66 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2319 helix: 1.83 (0.28), residues: 396 sheet: 0.10 (0.21), residues: 642 loop : -1.18 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 504 TYR 0.009 0.001 TYR H 100A PHE 0.027 0.002 PHE N 71 TRP 0.007 0.001 TRP E 45 HIS 0.003 0.000 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (20325) covalent geometry : angle 0.54360 / 0.27 (27573) SS BOND : bond 0.00237 / 0.17 ( 42) SS BOND : angle 0.56577 / 0.38 ( 84) hydrogen bonds : bond 0.03003 / 1.96 ( 657) hydrogen bonds : angle 4.66892 / 3.32 ( 1746) link_ALPHA1-2 : bond 0.00560 / 0.31 ( 9) link_ALPHA1-2 : angle 3.31321 / 2.39 ( 27) link_ALPHA1-3 : bond 0.00778 / 0.41 ( 9) link_ALPHA1-3 : angle 1.45634 / 0.88 ( 27) link_ALPHA1-6 : bond 0.00398 / 0.23 ( 6) link_ALPHA1-6 : angle 1.59093 / 1.01 ( 18) link_BETA1-4 : bond 0.00285 / 0.17 ( 18) link_BETA1-4 : angle 1.99622 / 1.32 ( 54) link_NAG-ASN : bond 0.00529 / 0.34 ( 54) link_NAG-ASN : angle 4.06395 / 2.67 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 312 time to evaluate : 0.801 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: E 161 MET cc_start: 0.8507 (tpp) cc_final: 0.7550 (tpt) REVERT: F 35 TRP cc_start: 0.8729 (m100) cc_final: 0.8339 (m100) REVERT: F 114 GLN cc_start: 0.8123 (tt0) cc_final: 0.7887 (tt0) REVERT: F 180 ASP cc_start: 0.9062 (m-30) cc_final: 0.8725 (t0) REVERT: F 289 ASN cc_start: 0.8229 (p0) cc_final: 0.7999 (p0) REVERT: F 365 SER cc_start: 0.8734 (p) cc_final: 0.8481 (t) REVERT: G 97 LYS cc_start: 0.8874 (tppt) cc_final: 0.8640 (mmtp) REVERT: G 161 MET cc_start: 0.8455 (tpp) cc_final: 0.8144 (tpt) REVERT: G 178 ARG cc_start: 0.8004 (tpt90) cc_final: 0.7789 (tpt90) REVERT: G 180 ASP cc_start: 0.8931 (m-30) cc_final: 0.8614 (t0) REVERT: J 100 LEU cc_start: 0.8881 (mt) cc_final: 0.8666 (mt) REVERT: K 82 ASP cc_start: 0.6720 (m-30) cc_final: 0.6031 (m-30) REVERT: N 26 SER cc_start: 0.8879 (m) cc_final: 0.8588 (m) REVERT: N 71 PHE cc_start: 0.8006 (m-10) cc_final: 0.7739 (m-10) outliers start: 48 outliers final: 30 residues processed: 345 average time/residue: 0.1372 time to fit residues: 75.9693 Evaluate side-chains 326 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 215 optimal weight: 0.0270 chunk 2 optimal weight: 0.0670 chunk 23 optimal weight: 6.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118608 restraints weight = 26323.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122187 restraints weight = 16257.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124584 restraints weight = 11769.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126179 restraints weight = 9436.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127196 restraints weight = 8085.401| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20463 Z= 0.186 Angle : 0.690 12.649 27945 Z= 0.319 Chirality : 0.049 0.401 3333 Planarity : 0.004 0.037 3402 Dihedral : 7.858 70.398 4506 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.34 % Allowed : 17.27 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2319 helix: 1.95 (0.28), residues: 378 sheet: -0.05 (0.21), residues: 642 loop : -1.30 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 504 TYR 0.014 0.001 TYR E 435 PHE 0.020 0.002 PHE N 83 TRP 0.011 0.001 TRP E 45 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (20325) covalent geometry : angle 0.60285 / 0.30 (27573) SS BOND : bond 0.00292 / 0.20 ( 42) SS BOND : angle 0.72281 / 0.48 ( 84) hydrogen bonds : bond 0.03275 / 2.14 ( 657) hydrogen bonds : angle 4.70346 / 3.35 ( 1746) link_ALPHA1-2 : bond 0.00429 / 0.24 ( 9) link_ALPHA1-2 : angle 3.28815 / 2.37 ( 27) link_ALPHA1-3 : bond 0.00732 / 0.37 ( 9) link_ALPHA1-3 : angle 1.59225 / 0.94 ( 27) link_ALPHA1-6 : bond 0.00233 / 0.13 ( 6) link_ALPHA1-6 : angle 1.71383 / 1.09 ( 18) link_BETA1-4 : bond 0.00255 / 0.15 ( 18) link_BETA1-4 : angle 1.94846 / 1.26 ( 54) link_NAG-ASN : bond 0.00432 / 0.28 ( 54) link_NAG-ASN : angle 4.03728 / 2.67 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 316 time to evaluate : 0.664 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: C 634 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: E 35 TRP cc_start: 0.8764 (m100) cc_final: 0.8406 (m100) REVERT: E 161 MET cc_start: 0.8610 (tpp) cc_final: 0.7525 (tpt) REVERT: E 234 ASN cc_start: 0.6276 (OUTLIER) cc_final: 0.5920 (p0) REVERT: F 35 TRP cc_start: 0.8909 (m100) cc_final: 0.8522 (m100) REVERT: F 114 GLN cc_start: 0.8179 (tt0) cc_final: 0.7968 (tt0) REVERT: F 180 ASP cc_start: 0.9097 (m-30) cc_final: 0.8785 (t0) REVERT: F 234 ASN cc_start: 0.6121 (OUTLIER) cc_final: 0.5650 (p0) REVERT: F 258 GLN cc_start: 0.8904 (mt0) cc_final: 0.8636 (tt0) REVERT: F 289 ASN cc_start: 0.8384 (p0) cc_final: 0.8084 (p0) REVERT: F 365 SER cc_start: 0.8785 (p) cc_final: 0.8534 (t) REVERT: G 97 LYS cc_start: 0.8888 (tppt) cc_final: 0.8676 (mmtp) REVERT: G 161 MET cc_start: 0.8601 (tpp) cc_final: 0.8207 (tpt) REVERT: G 180 ASP cc_start: 0.9003 (m-30) cc_final: 0.8705 (t0) REVERT: G 365 SER cc_start: 0.8914 (p) cc_final: 0.8688 (t) REVERT: G 486 TYR cc_start: 0.9105 (m-80) cc_final: 0.8695 (m-10) REVERT: H 50 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8234 (ttt90) REVERT: J 100 LEU cc_start: 0.8975 (mt) cc_final: 0.8753 (mt) REVERT: K 27 GLN cc_start: 0.7689 (pt0) cc_final: 0.7457 (pt0) REVERT: N 26 SER cc_start: 0.8873 (m) cc_final: 0.8576 (m) REVERT: N 71 PHE cc_start: 0.8219 (m-10) cc_final: 0.7833 (m-10) outliers start: 69 outliers final: 48 residues processed: 360 average time/residue: 0.1308 time to fit residues: 75.6259 Evaluate side-chains 349 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS G 258 GLN ** J 81 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 = 0.3692 r_free = 0.3692 target = 0.148238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120757 restraints weight = 26093.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124436 restraints weight = 15917.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126940 restraints weight = 11441.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128612 restraints weight = 9105.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129799 restraints weight = 7749.675| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20463 Z= 0.125 Angle : 0.640 16.547 27945 Z= 0.297 Chirality : 0.048 0.418 3333 Planarity : 0.003 0.047 3402 Dihedral : 7.378 64.052 4506 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.52 % Allowed : 19.01 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2319 helix: 1.82 (0.29), residues: 393 sheet: -0.04 (0.21), residues: 651 loop : -1.22 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 61 TYR 0.014 0.001 TYR F 486 PHE 0.027 0.002 PHE L 83 TRP 0.007 0.001 TRP E 45 HIS 0.004 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20325) covalent geometry : angle 0.54978 / 0.28 (27573) SS BOND : bond 0.00243 / 0.17 ( 42) SS BOND : angle 0.57915 / 0.38 ( 84) hydrogen bonds : bond 0.02976 / 1.93 ( 657) hydrogen bonds : angle 4.57436 / 3.25 ( 1746) link_ALPHA1-2 : bond 0.00625 / 0.34 ( 9) link_ALPHA1-2 : angle 3.32695 / 2.40 ( 27) link_ALPHA1-3 : bond 0.00860 / 0.45 ( 9) link_ALPHA1-3 : angle 1.51005 / 0.88 ( 27) link_ALPHA1-6 : bond 0.00506 / 0.30 ( 6) link_ALPHA1-6 : angle 1.57587 / 1.01 ( 18) link_BETA1-4 : bond 0.00213 / 0.13 ( 18) link_BETA1-4 : angle 1.85706 / 1.18 ( 54) link_NAG-ASN : bond 0.00367 / 0.24 ( 54) link_NAG-ASN : angle 3.91224 / 2.58 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 0.720 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: E 35 TRP cc_start: 0.8781 (m100) cc_final: 0.8420 (m100) REVERT: E 161 MET cc_start: 0.8551 (tpp) cc_final: 0.7566 (tpt) REVERT: E 234 ASN cc_start: 0.6041 (OUTLIER) cc_final: 0.5795 (p0) REVERT: F 35 TRP cc_start: 0.8802 (m100) cc_final: 0.8402 (m100) REVERT: F 114 GLN cc_start: 0.8117 (tt0) cc_final: 0.7909 (tt0) REVERT: F 180 ASP cc_start: 0.9015 (m-30) cc_final: 0.8806 (t0) REVERT: F 234 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.5707 (p0) REVERT: F 289 ASN cc_start: 0.8380 (p0) cc_final: 0.8074 (p0) REVERT: G 161 MET cc_start: 0.8580 (tpp) cc_final: 0.8209 (tpt) REVERT: G 180 ASP cc_start: 0.8883 (m-30) cc_final: 0.8661 (t0) REVERT: G 486 TYR cc_start: 0.9053 (m-80) cc_final: 0.8590 (m-10) REVERT: H 50 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8066 (ttt90) REVERT: H 76 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7836 (t0) REVERT: J 50 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7871 (ttt90) REVERT: J 100 LEU cc_start: 0.8940 (mt) cc_final: 0.8632 (mt) REVERT: N 26 SER cc_start: 0.8844 (m) cc_final: 0.8554 (m) REVERT: N 48 MET cc_start: 0.7406 (tmm) cc_final: 0.7137 (tmm) REVERT: N 71 PHE cc_start: 0.8271 (m-80) cc_final: 0.8038 (m-10) outliers start: 52 outliers final: 38 residues processed: 341 average time/residue: 0.1232 time to fit residues: 67.3417 Evaluate side-chains 335 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 102 THR 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 200 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 0.1980 chunk 169 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118871 restraints weight = 26197.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122500 restraints weight = 16129.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124951 restraints weight = 11656.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126621 restraints weight = 9317.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127670 restraints weight = 7967.530| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20463 Z= 0.163 Angle : 0.664 13.512 27945 Z= 0.309 Chirality : 0.050 0.531 3333 Planarity : 0.003 0.037 3402 Dihedral : 7.525 65.261 4506 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.24 % Allowed : 18.77 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2319 helix: 2.11 (0.29), residues: 372 sheet: -0.06 (0.21), residues: 645 loop : -1.34 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 504 TYR 0.012 0.001 TYR E 435 PHE 0.022 0.002 PHE L 83 TRP 0.010 0.001 TRP E 45 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (20325) covalent geometry : angle 0.57917 / 0.29 (27573) SS BOND : bond 0.00282 / 0.20 ( 42) SS BOND : angle 0.66834 / 0.44 ( 84) hydrogen bonds : bond 0.03093 / 2.01 ( 657) hydrogen bonds : angle 4.58752 / 3.27 ( 1746) link_ALPHA1-2 : bond 0.00506 / 0.28 ( 9) link_ALPHA1-2 : angle 3.31271 / 2.40 ( 27) link_ALPHA1-3 : bond 0.00747 / 0.38 ( 9) link_ALPHA1-3 : angle 1.56003 / 0.92 ( 27) link_ALPHA1-6 : bond 0.00368 / 0.21 ( 6) link_ALPHA1-6 : angle 1.63387 / 1.04 ( 18) link_BETA1-4 : bond 0.00230 / 0.14 ( 18) link_BETA1-4 : angle 1.80028 / 1.12 ( 54) link_NAG-ASN : bond 0.00493 / 0.33 ( 54) link_NAG-ASN : angle 3.88967 / 2.53 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 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: 67 poor density : 299 time to evaluate : 0.572 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: E 35 TRP cc_start: 0.8813 (m100) cc_final: 0.8420 (m100) REVERT: E 161 MET cc_start: 0.8601 (tpp) cc_final: 0.7605 (tpt) REVERT: F 35 TRP cc_start: 0.8826 (m100) cc_final: 0.8454 (m100) REVERT: F 114 GLN cc_start: 0.8151 (tt0) cc_final: 0.7943 (tt0) REVERT: F 180 ASP cc_start: 0.9006 (m-30) cc_final: 0.8787 (t0) REVERT: F 289 ASN cc_start: 0.8409 (p0) cc_final: 0.8113 (p0) REVERT: G 35 TRP cc_start: 0.8988 (m100) cc_final: 0.8680 (m100) REVERT: G 161 MET cc_start: 0.8601 (tpp) cc_final: 0.8140 (tpt) REVERT: G 180 ASP cc_start: 0.8855 (m-30) cc_final: 0.8636 (t0) REVERT: G 486 TYR cc_start: 0.9090 (m-80) cc_final: 0.8684 (m-10) REVERT: H 50 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8131 (ttt90) REVERT: H 76 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7696 (t0) REVERT: J 50 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8076 (ttt90) REVERT: J 76 ASN cc_start: 0.8107 (t0) cc_final: 0.7816 (t0) REVERT: J 100 LEU cc_start: 0.8980 (mt) cc_final: 0.8691 (mt) REVERT: M 50 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8099 (ttt180) REVERT: N 13 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7931 (pp) REVERT: N 26 SER cc_start: 0.8812 (m) cc_final: 0.8516 (m) REVERT: N 71 PHE cc_start: 0.8259 (m-80) cc_final: 0.8008 (m-10) outliers start: 67 outliers final: 54 residues processed: 342 average time/residue: 0.1131 time to fit residues: 62.1648 Evaluate side-chains 347 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 161 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN A 652 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120783 restraints weight = 26126.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124478 restraints weight = 15922.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126950 restraints weight = 11461.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128571 restraints weight = 9154.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129791 restraints weight = 7828.016| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20463 Z= 0.123 Angle : 0.645 20.914 27945 Z= 0.297 Chirality : 0.048 0.398 3333 Planarity : 0.003 0.037 3402 Dihedral : 7.319 60.961 4506 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.81 % Allowed : 19.64 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.18), residues: 2319 helix: 1.86 (0.29), residues: 393 sheet: 0.00 (0.21), residues: 645 loop : -1.20 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 504 TYR 0.010 0.001 TYR C 638 PHE 0.020 0.002 PHE G 53 TRP 0.007 0.001 TRP E 45 HIS 0.004 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (20325) covalent geometry : angle 0.55260 / 0.28 (27573) SS BOND : bond 0.00238 / 0.17 ( 42) SS BOND : angle 0.56845 / 0.36 ( 84) hydrogen bonds : bond 0.02914 / 1.89 ( 657) hydrogen bonds : angle 4.50304 / 3.21 ( 1746) link_ALPHA1-2 : bond 0.00639 / 0.35 ( 9) link_ALPHA1-2 : angle 3.34093 / 2.41 ( 27) link_ALPHA1-3 : bond 0.00816 / 0.43 ( 9) link_ALPHA1-3 : angle 1.48494 / 0.87 ( 27) link_ALPHA1-6 : bond 0.00552 / 0.33 ( 6) link_ALPHA1-6 : angle 1.56366 / 1.01 ( 18) link_BETA1-4 : bond 0.00215 / 0.13 ( 18) link_BETA1-4 : angle 1.74978 / 1.07 ( 54) link_NAG-ASN : bond 0.00454 / 0.30 ( 54) link_NAG-ASN : angle 4.01422 / 2.56 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 307 time to evaluate : 0.705 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: C 634 GLU cc_start: 0.7163 (mp0) cc_final: 0.6935 (mp0) REVERT: E 35 TRP cc_start: 0.8796 (m100) cc_final: 0.8416 (m100) REVERT: E 161 MET cc_start: 0.8552 (tpp) cc_final: 0.7628 (tpt) REVERT: E 368 ASP cc_start: 0.6966 (t0) cc_final: 0.6725 (t0) REVERT: F 35 TRP cc_start: 0.8794 (m100) cc_final: 0.8420 (m100) REVERT: F 114 GLN cc_start: 0.8108 (tt0) cc_final: 0.7905 (tt0) REVERT: F 289 ASN cc_start: 0.8385 (p0) cc_final: 0.8116 (p0) REVERT: G 35 TRP cc_start: 0.8962 (m100) cc_final: 0.8618 (m100) REVERT: G 161 MET cc_start: 0.8578 (tpp) cc_final: 0.8136 (tpt) REVERT: G 180 ASP cc_start: 0.8800 (m-30) cc_final: 0.8597 (t0) REVERT: H 50 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7966 (ttt90) REVERT: H 76 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7774 (t0) REVERT: J 50 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7870 (ttt90) REVERT: J 76 ASN cc_start: 0.8130 (t0) cc_final: 0.7845 (t0) REVERT: J 100 LEU cc_start: 0.8979 (mt) cc_final: 0.8679 (mt) REVERT: M 50 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8044 (ttt90) REVERT: N 13 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7963 (pp) REVERT: N 26 SER cc_start: 0.8777 (m) cc_final: 0.8476 (m) REVERT: N 48 MET cc_start: 0.7417 (tmm) cc_final: 0.7173 (tmm) REVERT: N 71 PHE cc_start: 0.8281 (m-80) cc_final: 0.8044 (m-10) outliers start: 58 outliers final: 47 residues processed: 348 average time/residue: 0.1130 time to fit residues: 63.4216 Evaluate side-chains 344 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 93 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** J 81 GLN ** 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 = 0.3692 r_free = 0.3692 target = 0.148074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120784 restraints weight = 25888.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124455 restraints weight = 15860.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126901 restraints weight = 11423.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128603 restraints weight = 9131.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129782 restraints weight = 7784.612| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20463 Z= 0.126 Angle : 0.649 17.781 27945 Z= 0.298 Chirality : 0.049 0.504 3333 Planarity : 0.003 0.037 3402 Dihedral : 7.113 59.921 4506 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.95 % Allowed : 19.69 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2319 helix: 2.24 (0.29), residues: 375 sheet: 0.04 (0.21), residues: 651 loop : -1.26 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 504 TYR 0.009 0.001 TYR C 638 PHE 0.019 0.002 PHE G 53 TRP 0.010 0.001 TRP F 45 HIS 0.004 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (20325) covalent geometry : angle 0.55984 / 0.28 (27573) SS BOND : bond 0.00258 / 0.18 ( 42) SS BOND : angle 0.70414 / 0.47 ( 84) hydrogen bonds : bond 0.02913 / 1.90 ( 657) hydrogen bonds : angle 4.47253 / 3.18 ( 1746) link_ALPHA1-2 : bond 0.00621 / 0.34 ( 9) link_ALPHA1-2 : angle 3.32562 / 2.40 ( 27) link_ALPHA1-3 : bond 0.00799 / 0.42 ( 9) link_ALPHA1-3 : angle 1.46640 / 0.86 ( 27) link_ALPHA1-6 : bond 0.00553 / 0.33 ( 6) link_ALPHA1-6 : angle 1.56209 / 1.00 ( 18) link_BETA1-4 : bond 0.00228 / 0.14 ( 18) link_BETA1-4 : angle 1.69495 / 1.04 ( 54) link_NAG-ASN : bond 0.00505 / 0.35 ( 54) link_NAG-ASN : angle 3.95836 / 2.62 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 0.458 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: E 35 TRP cc_start: 0.8794 (m100) cc_final: 0.8410 (m100) REVERT: E 161 MET cc_start: 0.8584 (tpp) cc_final: 0.7673 (tpt) REVERT: E 368 ASP cc_start: 0.6999 (t0) cc_final: 0.6731 (t0) REVERT: F 35 TRP cc_start: 0.8808 (m100) cc_final: 0.8438 (m100) REVERT: F 114 GLN cc_start: 0.8103 (tt0) cc_final: 0.7898 (tt0) REVERT: F 289 ASN cc_start: 0.8391 (p0) cc_final: 0.8120 (p0) REVERT: G 35 TRP cc_start: 0.8991 (m100) cc_final: 0.8618 (m100) REVERT: G 161 MET cc_start: 0.8558 (tpp) cc_final: 0.8115 (tpt) REVERT: H 50 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7956 (ttt90) REVERT: H 76 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7808 (t0) REVERT: J 50 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7860 (ttt90) REVERT: J 76 ASN cc_start: 0.8197 (t0) cc_final: 0.7906 (t0) REVERT: J 100 LEU cc_start: 0.8972 (mt) cc_final: 0.8669 (mt) REVERT: K 61 ARG cc_start: 0.8732 (mtm180) cc_final: 0.8429 (mtm180) REVERT: M 50 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8033 (ttt90) REVERT: N 13 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7923 (pp) REVERT: N 26 SER cc_start: 0.8757 (m) cc_final: 0.8466 (m) REVERT: N 71 PHE cc_start: 0.8283 (m-80) cc_final: 0.8042 (m-10) outliers start: 61 outliers final: 48 residues processed: 340 average time/residue: 0.1153 time to fit residues: 63.3660 Evaluate side-chains 343 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 59 optimal weight: 0.1980 chunk 222 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 125 optimal weight: 30.0000 chunk 218 optimal weight: 3.9990 chunk 217 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122357 restraints weight = 26017.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126069 restraints weight = 15924.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128586 restraints weight = 11441.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130292 restraints weight = 9095.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131392 restraints weight = 7728.548| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20463 Z= 0.110 Angle : 0.620 17.523 27945 Z= 0.287 Chirality : 0.048 0.396 3333 Planarity : 0.003 0.037 3402 Dihedral : 6.818 55.814 4506 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.47 % Allowed : 20.27 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2319 helix: 2.39 (0.29), residues: 372 sheet: 0.13 (0.21), residues: 642 loop : -1.20 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 504 TYR 0.011 0.001 TYR C 638 PHE 0.020 0.002 PHE M 67 TRP 0.015 0.001 TRP C 631 HIS 0.003 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20325) covalent geometry : angle 0.54026 / 0.27 (27573) SS BOND : bond 0.00224 / 0.16 ( 42) SS BOND : angle 0.58270 / 0.39 ( 84) hydrogen bonds : bond 0.02805 / 1.81 ( 657) hydrogen bonds : angle 4.41874 / 3.15 ( 1746) link_ALPHA1-2 : bond 0.00690 / 0.38 ( 9) link_ALPHA1-2 : angle 3.35053 / 2.41 ( 27) link_ALPHA1-3 : bond 0.00837 / 0.45 ( 9) link_ALPHA1-3 : angle 1.40623 / 0.82 ( 27) link_ALPHA1-6 : bond 0.00682 / 0.41 ( 6) link_ALPHA1-6 : angle 1.53607 / 1.00 ( 18) link_BETA1-4 : bond 0.00242 / 0.14 ( 18) link_BETA1-4 : angle 1.63257 / 1.00 ( 54) link_NAG-ASN : bond 0.00480 / 0.33 ( 54) link_NAG-ASN : angle 3.62001 / 2.38 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: E 35 TRP cc_start: 0.8770 (m100) cc_final: 0.8399 (m100) REVERT: E 161 MET cc_start: 0.8563 (tpp) cc_final: 0.7604 (tpt) REVERT: E 368 ASP cc_start: 0.6943 (t0) cc_final: 0.6704 (t0) REVERT: E 486 TYR cc_start: 0.8996 (m-10) cc_final: 0.8764 (m-80) REVERT: F 35 TRP cc_start: 0.8773 (m100) cc_final: 0.8446 (m100) REVERT: F 289 ASN cc_start: 0.8374 (p0) cc_final: 0.8114 (p0) REVERT: F 434 MET cc_start: 0.7218 (ttm) cc_final: 0.6670 (ttm) REVERT: G 35 TRP cc_start: 0.8972 (m100) cc_final: 0.8610 (m100) REVERT: H 50 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7960 (ttt90) REVERT: H 76 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7734 (t0) REVERT: J 50 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7819 (ttt90) REVERT: J 76 ASN cc_start: 0.8201 (t0) cc_final: 0.7912 (t0) REVERT: J 100 LEU cc_start: 0.8960 (mt) cc_final: 0.8660 (mt) REVERT: K 61 ARG cc_start: 0.8713 (mtm180) cc_final: 0.8425 (mtm180) REVERT: L 71 PHE cc_start: 0.8465 (m-80) cc_final: 0.8088 (m-10) REVERT: M 50 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7593 (ttt90) REVERT: N 13 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7963 (pp) REVERT: N 26 SER cc_start: 0.8735 (m) cc_final: 0.8479 (m) REVERT: N 71 PHE cc_start: 0.8275 (m-80) cc_final: 0.8021 (m-10) outliers start: 51 outliers final: 41 residues processed: 346 average time/residue: 0.1271 time to fit residues: 70.6537 Evaluate side-chains 338 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 292 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 50 ARG Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 8 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 135 optimal weight: 0.4980 chunk 225 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 173 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122614 restraints weight = 26115.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126306 restraints weight = 15915.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128832 restraints weight = 11441.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130537 restraints weight = 9090.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131618 restraints weight = 7738.054| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20463 Z= 0.112 Angle : 0.614 16.892 27945 Z= 0.285 Chirality : 0.048 0.396 3333 Planarity : 0.003 0.036 3402 Dihedral : 6.689 53.976 4506 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.27 % Allowed : 20.56 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.18), residues: 2319 helix: 2.41 (0.29), residues: 372 sheet: 0.14 (0.21), residues: 642 loop : -1.21 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 504 TYR 0.010 0.001 TYR C 638 PHE 0.018 0.002 PHE G 53 TRP 0.013 0.001 TRP E 338 HIS 0.003 0.000 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20325) covalent geometry : angle 0.54117 / 0.27 (27573) SS BOND : bond 0.00279 / 0.20 ( 42) SS BOND : angle 0.56306 / 0.38 ( 84) hydrogen bonds : bond 0.02796 / 1.80 ( 657) hydrogen bonds : angle 4.35761 / 3.10 ( 1746) link_ALPHA1-2 : bond 0.00660 / 0.37 ( 9) link_ALPHA1-2 : angle 3.34557 / 2.41 ( 27) link_ALPHA1-3 : bond 0.00820 / 0.44 ( 9) link_ALPHA1-3 : angle 1.38531 / 0.82 ( 27) link_ALPHA1-6 : bond 0.00699 / 0.42 ( 6) link_ALPHA1-6 : angle 1.54134 / 1.00 ( 18) link_BETA1-4 : bond 0.00250 / 0.15 ( 18) link_BETA1-4 : angle 1.58522 / 0.97 ( 54) link_NAG-ASN : bond 0.00448 / 0.30 ( 54) link_NAG-ASN : angle 3.43124 / 2.26 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3257.54 seconds wall clock time: 57 minutes 13.68 seconds (3433.68 seconds total)