Starting phenix.real_space_refine on Tue Jun 17 18:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb2_40288/06_2025/8sb2_40288_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb2_40288/06_2025/8sb2_40288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sb2_40288/06_2025/8sb2_40288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb2_40288/06_2025/8sb2_40288.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb2_40288/06_2025/8sb2_40288_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb2_40288/06_2025/8sb2_40288_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.010 sd= 0.240 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 141 5.16 5 C 12585 2.51 5 N 3321 2.21 5 O 4139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20186 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain: "L" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "T" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.29, per 1000 atoms: 0.61 Number of scatterers: 20186 At special positions: 0 Unit cell: (159.84, 156.6, 139.32, 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 141 16.00 O 4139 8.00 N 3321 7.00 C 12585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " 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 F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " 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 Atom "HETATM19206 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN O 8 " - " MAN O 9 " " MAN O 10 " - " MAN O 11 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN T 10 " - " MAN T 11 " " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-6 " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 10 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 10 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG E 1 " - " ASN A 138 " " NAG J 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 442 " " NAG R 1 " - " ASN F 138 " " NAG S 1 " - " ASN F 301 " " NAG T 1 " - " ASN F 332 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 442 " " NAG W 1 " - " ASN K 138 " " NAG X 1 " - " ASN K 301 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 156 " " NAG a 1 " - " ASN K 442 " Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 2.5 seconds 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4554 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 45 sheets defined 17.4% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.680A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.797A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.503A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.734A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.893A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.602A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.631A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.233A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 649 through 663 removed outlier: 3.985A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.941A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.677A pdb=" N ALA F 60 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 removed outlier: 3.787A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA F 73 " --> pdb=" O TRP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.537A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.736A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.765A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 596 removed outlier: 3.632A pdb=" N GLN G 575 " --> pdb=" O TRP G 571 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 585 " --> pdb=" O LEU G 581 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 593 " --> pdb=" O ASP G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.680A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.030A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 646 Processing helix chain 'G' and resid 650 through 654 Processing helix chain 'G' and resid 655 through 662 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.525A pdb=" N ASP I 84 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.692A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 74 removed outlier: 3.791A pdb=" N HIS K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 475 through 481 removed outlier: 3.767A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 543 removed outlier: 3.926A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.565A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN L 577 " --> pdb=" O ILE L 573 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG L 585 " --> pdb=" O LEU L 581 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP L 589 " --> pdb=" O ARG L 585 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 593 " --> pdb=" O ASP L 589 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY L 594 " --> pdb=" O GLN L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 removed outlier: 3.650A pdb=" N SER L 615 " --> pdb=" O SER L 612 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.148A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 646 Processing helix chain 'L' and resid 649 through 663 removed outlier: 3.659A pdb=" N GLN L 653 " --> pdb=" O SER L 649 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.550A pdb=" N ASP N 84 " --> pdb=" O GLN N 81 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.063A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 6.694A pdb=" N MET A 154 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 134 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.621A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.545A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.841A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.841A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.637A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 361 removed outlier: 3.600A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.151A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.526A pdb=" N THR D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.526A pdb=" N THR D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.495A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.514A pdb=" N LEU F 84 " --> pdb=" O THR F 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 177 removed outlier: 6.759A pdb=" N MET F 154 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA F 134 " --> pdb=" O MET F 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.560A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.568A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.046A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.587A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 359 through 361 removed outlier: 3.597A pdb=" N GLY F 393 " --> pdb=" O TYR F 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.016A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.511A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.511A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 17 through 23 removed outlier: 3.541A pdb=" N THR I 72 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.242A pdb=" N VAL L 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL K 38 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR L 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR K 40 " --> pdb=" O CYS L 604 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS L 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'K' and resid 169 through 177 removed outlier: 6.682A pdb=" N MET K 154 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA K 134 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.540A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 6.569A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.032A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AE4, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.631A pdb=" N GLY K 393 " --> pdb=" O TYR K 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.170A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.524A pdb=" N THR N 108 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL N 35 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR N 51 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.524A pdb=" N THR N 108 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.537A pdb=" N THR N 72 " --> pdb=" O SER N 69 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1821 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: 6.69 Time building geometry restraints manager: 6.55 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: 6211 1.34 - 1.46: 5249 1.46 - 1.59: 8953 1.59 - 1.71: 1 1.71 - 1.84: 192 Bond restraints: 20606 Sorted by residual: bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.01e+01 bond pdb=" C THR F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.76e+01 bond pdb=" C1 MAN T 11 " pdb=" C2 MAN T 11 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C5 MAN Y 7 " pdb=" O5 MAN Y 7 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C5 MAN O 7 " pdb=" O5 MAN O 7 " ideal model delta sigma weight residual 1.418 1.481 -0.063 2.00e-02 2.50e+03 9.78e+00 ... (remaining 20601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 27260 3.01 - 6.03: 653 6.03 - 9.04: 107 9.04 - 12.06: 5 12.06 - 15.07: 4 Bond angle restraints: 28029 Sorted by residual: angle pdb=" C ASN K 138 " pdb=" CA ASN K 138 " pdb=" CB ASN K 138 " ideal model delta sigma weight residual 111.82 120.72 -8.90 1.28e+00 6.10e-01 4.84e+01 angle pdb=" N ASP D 33 " pdb=" CA ASP D 33 " pdb=" C ASP D 33 " ideal model delta sigma weight residual 113.17 104.56 8.61 1.26e+00 6.30e-01 4.67e+01 angle pdb=" N ASP N 33 " pdb=" CA ASP N 33 " pdb=" C ASP N 33 " ideal model delta sigma weight residual 113.17 104.71 8.46 1.26e+00 6.30e-01 4.51e+01 angle pdb=" N SER B 649 " pdb=" CA SER B 649 " pdb=" C SER B 649 " ideal model delta sigma weight residual 110.06 119.45 -9.39 1.43e+00 4.89e-01 4.31e+01 angle pdb=" N ASP I 33 " pdb=" CA ASP I 33 " pdb=" C ASP I 33 " ideal model delta sigma weight residual 113.28 105.37 7.91 1.22e+00 6.72e-01 4.21e+01 ... (remaining 28024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 12606 23.11 - 46.21: 493 46.21 - 69.31: 101 69.31 - 92.42: 97 92.42 - 115.52: 48 Dihedral angle restraints: 13345 sinusoidal: 6220 harmonic: 7125 Sorted by residual: dihedral pdb=" CB CYS K 501 " pdb=" SG CYS K 501 " pdb=" SG CYS L 605 " pdb=" CB CYS L 605 " ideal model delta sinusoidal sigma weight residual 93.00 27.72 65.28 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA GLY K 431 " pdb=" C GLY K 431 " pdb=" N ARG K 432 " pdb=" CA ARG K 432 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -146.90 -33.10 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 13342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2710 0.070 - 0.139: 554 0.139 - 0.209: 100 0.209 - 0.278: 22 0.278 - 0.348: 12 Chirality restraints: 3398 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.62e+00 chirality pdb=" CB VAL L 513 " pdb=" CA VAL L 513 " pdb=" CG1 VAL L 513 " pdb=" CG2 VAL L 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 3395 not shown) Planarity restraints: 3471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.001 2.00e-02 2.50e+03 6.40e-02 5.12e+01 pdb=" CG ASN A 138 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 156 " -0.027 2.00e-02 2.50e+03 2.46e-02 7.58e+00 pdb=" CG ASN K 156 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN K 156 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN K 156 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Z 1 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 178 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO F 179 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 179 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 179 " 0.038 5.00e-02 4.00e+02 ... (remaining 3468 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4545 2.79 - 3.32: 17566 3.32 - 3.85: 32311 3.85 - 4.37: 37854 4.37 - 4.90: 66433 Nonbonded interactions: 158709 Sorted by model distance: nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP K 325 " pdb=" OH TYR M 33 " model vdw 2.271 3.040 nonbonded pdb=" O MET K 369 " pdb=" OG1 THR K 373 " model vdw 2.273 3.040 nonbonded pdb=" O MET F 369 " pdb=" OG1 THR F 373 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR N 48 " pdb=" O3 MAN Y 5 " model vdw 2.288 3.040 ... (remaining 158704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'U' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'V' 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: 1.620 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: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.160 Process input model: 45.730 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.120 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.006 0.075 20733 Z= 0.321 Angle : 1.162 30.074 28365 Z= 0.590 Chirality : 0.063 0.348 3398 Planarity : 0.007 0.087 3456 Dihedral : 16.754 115.525 8656 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2454 helix: -2.95 (0.20), residues: 375 sheet: -0.06 (0.19), residues: 744 loop : -1.71 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 45 HIS 0.010 0.001 HIS M 116 PHE 0.012 0.002 PHE K 376 TYR 0.024 0.002 TYR M 27 ARG 0.017 0.001 ARG L 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 15) link_NAG-ASN : angle 7.03694 ( 45) link_ALPHA1-6 : bond 0.00698 ( 14) link_ALPHA1-6 : angle 2.25093 ( 42) link_BETA1-4 : bond 0.01466 ( 27) link_BETA1-4 : angle 3.91328 ( 81) link_ALPHA1-2 : bond 0.00975 ( 14) link_ALPHA1-2 : angle 2.72986 ( 42) link_ALPHA1-3 : bond 0.00931 ( 12) link_ALPHA1-3 : angle 1.85466 ( 36) hydrogen bonds : bond 0.15952 ( 653) hydrogen bonds : angle 8.12926 ( 1821) SS BOND : bond 0.00304 ( 45) SS BOND : angle 1.53652 ( 90) covalent geometry : bond 0.00639 (20606) covalent geometry : angle 1.10040 (28029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8965 (mtp) cc_final: 0.8618 (mtp) REVERT: A 426 MET cc_start: 0.7231 (ptt) cc_final: 0.6370 (tpt) REVERT: C 25 SER cc_start: 0.7710 (p) cc_final: 0.6851 (p) REVERT: F 34 LEU cc_start: 0.6165 (mt) cc_final: 0.5913 (pt) REVERT: L 584 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7585 (mm-30) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.5098 time to fit residues: 190.1304 Evaluate side-chains 178 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 190 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS C 13 ASN F 105 HIS F 374 HIS G 543 ASN K 105 HIS K 374 HIS N 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.171514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.166221 restraints weight = 28803.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.165729 restraints weight = 47056.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.164482 restraints weight = 46793.520| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20733 Z= 0.154 Angle : 0.735 11.898 28365 Z= 0.362 Chirality : 0.048 0.273 3398 Planarity : 0.005 0.052 3456 Dihedral : 13.071 95.124 4276 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 1.13 % Allowed : 5.87 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2454 helix: -2.34 (0.22), residues: 372 sheet: -0.02 (0.19), residues: 726 loop : -1.40 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 50 HIS 0.003 0.001 HIS A 330 PHE 0.011 0.002 PHE N 93 TYR 0.024 0.001 TYR I 51 ARG 0.004 0.000 ARG L 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 15) link_NAG-ASN : angle 4.17120 ( 45) link_ALPHA1-6 : bond 0.00630 ( 14) link_ALPHA1-6 : angle 1.95375 ( 42) link_BETA1-4 : bond 0.00877 ( 27) link_BETA1-4 : angle 2.76120 ( 81) link_ALPHA1-2 : bond 0.01074 ( 14) link_ALPHA1-2 : angle 2.13031 ( 42) link_ALPHA1-3 : bond 0.01085 ( 12) link_ALPHA1-3 : angle 1.75696 ( 36) hydrogen bonds : bond 0.04559 ( 653) hydrogen bonds : angle 6.29093 ( 1821) SS BOND : bond 0.00657 ( 45) SS BOND : angle 0.79173 ( 90) covalent geometry : bond 0.00338 (20606) covalent geometry : angle 0.69194 (28029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 5.754 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8991 (mtp) cc_final: 0.8649 (mtp) REVERT: I 25 THR cc_start: 0.8808 (t) cc_final: 0.8582 (m) REVERT: L 584 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7509 (mm-30) outliers start: 24 outliers final: 21 residues processed: 214 average time/residue: 0.4498 time to fit residues: 154.2515 Evaluate side-chains 199 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 33 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165881 restraints weight = 28736.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157194 restraints weight = 48687.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.154043 restraints weight = 47157.706| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20733 Z= 0.139 Angle : 0.693 9.992 28365 Z= 0.337 Chirality : 0.047 0.228 3398 Planarity : 0.004 0.047 3456 Dihedral : 10.571 89.851 4276 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.78 % Rotamer: Outliers : 1.83 % Allowed : 9.34 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2454 helix: -1.84 (0.24), residues: 372 sheet: 0.03 (0.19), residues: 726 loop : -1.23 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 50 HIS 0.006 0.001 HIS F 72 PHE 0.011 0.002 PHE D 93 TYR 0.026 0.001 TYR I 51 ARG 0.005 0.000 ARG I 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 15) link_NAG-ASN : angle 3.71243 ( 45) link_ALPHA1-6 : bond 0.00665 ( 14) link_ALPHA1-6 : angle 1.89438 ( 42) link_BETA1-4 : bond 0.00779 ( 27) link_BETA1-4 : angle 2.51847 ( 81) link_ALPHA1-2 : bond 0.01018 ( 14) link_ALPHA1-2 : angle 1.98837 ( 42) link_ALPHA1-3 : bond 0.01252 ( 12) link_ALPHA1-3 : angle 1.60323 ( 36) hydrogen bonds : bond 0.03971 ( 653) hydrogen bonds : angle 5.72292 ( 1821) SS BOND : bond 0.00198 ( 45) SS BOND : angle 0.69232 ( 90) covalent geometry : bond 0.00312 (20606) covalent geometry : angle 0.65551 (28029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9046 (mtp) cc_final: 0.8720 (mtp) REVERT: A 426 MET cc_start: 0.7215 (tpt) cc_final: 0.6974 (tpp) REVERT: B 542 ARG cc_start: 0.6896 (tpp-160) cc_final: 0.6671 (tpp-160) REVERT: B 629 LEU cc_start: 0.6519 (tp) cc_final: 0.6121 (pp) REVERT: H 25 SER cc_start: 0.7603 (p) cc_final: 0.7041 (p) REVERT: I 25 THR cc_start: 0.8822 (t) cc_final: 0.8596 (m) outliers start: 39 outliers final: 24 residues processed: 216 average time/residue: 0.3120 time to fit residues: 108.2357 Evaluate side-chains 205 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 239 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161254 restraints weight = 29035.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149544 restraints weight = 58543.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146637 restraints weight = 52475.165| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20733 Z= 0.221 Angle : 0.774 9.167 28365 Z= 0.376 Chirality : 0.050 0.200 3398 Planarity : 0.005 0.052 3456 Dihedral : 10.093 91.719 4276 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.40 % Favored : 93.44 % Rotamer: Outliers : 2.82 % Allowed : 10.75 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2454 helix: -1.89 (0.24), residues: 384 sheet: -0.10 (0.18), residues: 753 loop : -1.29 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 50 HIS 0.006 0.002 HIS H 35 PHE 0.014 0.002 PHE K 376 TYR 0.023 0.002 TYR I 48 ARG 0.007 0.001 ARG K 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 15) link_NAG-ASN : angle 4.22453 ( 45) link_ALPHA1-6 : bond 0.00535 ( 14) link_ALPHA1-6 : angle 1.94372 ( 42) link_BETA1-4 : bond 0.00702 ( 27) link_BETA1-4 : angle 2.60489 ( 81) link_ALPHA1-2 : bond 0.00918 ( 14) link_ALPHA1-2 : angle 2.00835 ( 42) link_ALPHA1-3 : bond 0.01037 ( 12) link_ALPHA1-3 : angle 1.85104 ( 36) hydrogen bonds : bond 0.04353 ( 653) hydrogen bonds : angle 5.87142 ( 1821) SS BOND : bond 0.00260 ( 45) SS BOND : angle 0.67018 ( 90) covalent geometry : bond 0.00536 (20606) covalent geometry : angle 0.73506 (28029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9022 (mtp) cc_final: 0.8788 (mtp) REVERT: C 34 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8081 (mt) REVERT: I 25 THR cc_start: 0.8722 (t) cc_final: 0.8495 (m) REVERT: I 33 ASP cc_start: 0.7761 (t0) cc_final: 0.7461 (t0) outliers start: 60 outliers final: 42 residues processed: 222 average time/residue: 0.3196 time to fit residues: 113.1766 Evaluate side-chains 218 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 72 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 199 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 202 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS F 287 HIS I 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.169607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.164166 restraints weight = 29028.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.159236 restraints weight = 50602.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155753 restraints weight = 62807.412| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20733 Z= 0.137 Angle : 0.684 9.660 28365 Z= 0.331 Chirality : 0.046 0.188 3398 Planarity : 0.004 0.043 3456 Dihedral : 9.253 85.594 4276 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.99 % Rotamer: Outliers : 2.86 % Allowed : 11.92 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2454 helix: -1.60 (0.24), residues: 384 sheet: -0.11 (0.18), residues: 750 loop : -1.16 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 112 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.002 PHE F 391 TYR 0.019 0.001 TYR I 48 ARG 0.004 0.000 ARG M 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 15) link_NAG-ASN : angle 3.68707 ( 45) link_ALPHA1-6 : bond 0.00560 ( 14) link_ALPHA1-6 : angle 1.84729 ( 42) link_BETA1-4 : bond 0.00694 ( 27) link_BETA1-4 : angle 2.36539 ( 81) link_ALPHA1-2 : bond 0.00916 ( 14) link_ALPHA1-2 : angle 1.92878 ( 42) link_ALPHA1-3 : bond 0.01100 ( 12) link_ALPHA1-3 : angle 1.72544 ( 36) hydrogen bonds : bond 0.03780 ( 653) hydrogen bonds : angle 5.55719 ( 1821) SS BOND : bond 0.00200 ( 45) SS BOND : angle 0.61051 ( 90) covalent geometry : bond 0.00310 (20606) covalent geometry : angle 0.64769 (28029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8980 (mtp) cc_final: 0.8429 (mtp) REVERT: F 348 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: G 530 MET cc_start: 0.8131 (mmm) cc_final: 0.7278 (mtt) REVERT: I 25 THR cc_start: 0.8770 (t) cc_final: 0.8524 (m) REVERT: M 3 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7498 (pt0) outliers start: 61 outliers final: 40 residues processed: 226 average time/residue: 0.3035 time to fit residues: 110.6047 Evaluate side-chains 216 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 167 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 239 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN I 16 GLN K 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.164961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.159446 restraints weight = 28884.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.147554 restraints weight = 61495.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143881 restraints weight = 70665.366| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20733 Z= 0.243 Angle : 0.802 21.187 28365 Z= 0.387 Chirality : 0.052 0.747 3398 Planarity : 0.005 0.049 3456 Dihedral : 9.692 91.205 4276 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.52 % Favored : 93.28 % Rotamer: Outliers : 3.47 % Allowed : 12.11 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2454 helix: -1.86 (0.23), residues: 402 sheet: -0.16 (0.18), residues: 759 loop : -1.34 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 50 HIS 0.007 0.002 HIS H 35 PHE 0.015 0.002 PHE F 317 TYR 0.019 0.002 TYR I 48 ARG 0.005 0.001 ARG C 57 Details of bonding type rmsd link_NAG-ASN : bond 0.01173 ( 15) link_NAG-ASN : angle 5.24808 ( 45) link_ALPHA1-6 : bond 0.00490 ( 14) link_ALPHA1-6 : angle 1.92208 ( 42) link_BETA1-4 : bond 0.00694 ( 27) link_BETA1-4 : angle 2.45059 ( 81) link_ALPHA1-2 : bond 0.00877 ( 14) link_ALPHA1-2 : angle 1.96934 ( 42) link_ALPHA1-3 : bond 0.01037 ( 12) link_ALPHA1-3 : angle 1.86592 ( 36) hydrogen bonds : bond 0.04431 ( 653) hydrogen bonds : angle 5.83625 ( 1821) SS BOND : bond 0.00291 ( 45) SS BOND : angle 0.68375 ( 90) covalent geometry : bond 0.00590 (20606) covalent geometry : angle 0.75592 (28029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9024 (mtp) cc_final: 0.8813 (mtp) REVERT: B 534 SER cc_start: 0.7722 (t) cc_final: 0.7439 (m) REVERT: H 50 TRP cc_start: 0.8134 (OUTLIER) cc_final: 0.6188 (p90) REVERT: H 85 SER cc_start: 0.7521 (t) cc_final: 0.7293 (p) REVERT: I 33 ASP cc_start: 0.7908 (t0) cc_final: 0.7578 (t0) REVERT: M 3 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: M 50 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.6741 (p90) outliers start: 74 outliers final: 56 residues processed: 237 average time/residue: 0.2708 time to fit residues: 104.1650 Evaluate side-chains 238 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 50 TRP Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 53 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 182 optimal weight: 0.0370 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.164094 restraints weight = 28675.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154142 restraints weight = 46289.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150937 restraints weight = 51144.966| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20733 Z= 0.123 Angle : 0.691 19.612 28365 Z= 0.333 Chirality : 0.047 0.517 3398 Planarity : 0.004 0.042 3456 Dihedral : 8.938 82.842 4276 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.23 % Rotamer: Outliers : 2.63 % Allowed : 13.62 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2454 helix: -1.38 (0.25), residues: 384 sheet: -0.09 (0.19), residues: 741 loop : -1.09 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.003 0.001 HIS F 72 PHE 0.010 0.001 PHE F 391 TYR 0.015 0.001 TYR D 48 ARG 0.004 0.000 ARG N 63 Details of bonding type rmsd link_NAG-ASN : bond 0.01106 ( 15) link_NAG-ASN : angle 5.12935 ( 45) link_ALPHA1-6 : bond 0.00532 ( 14) link_ALPHA1-6 : angle 1.79798 ( 42) link_BETA1-4 : bond 0.00695 ( 27) link_BETA1-4 : angle 2.16202 ( 81) link_ALPHA1-2 : bond 0.00882 ( 14) link_ALPHA1-2 : angle 1.86759 ( 42) link_ALPHA1-3 : bond 0.01129 ( 12) link_ALPHA1-3 : angle 1.71227 ( 36) hydrogen bonds : bond 0.03682 ( 653) hydrogen bonds : angle 5.43525 ( 1821) SS BOND : bond 0.00188 ( 45) SS BOND : angle 0.59826 ( 90) covalent geometry : bond 0.00266 (20606) covalent geometry : angle 0.64200 (28029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 348 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: G 530 MET cc_start: 0.8114 (mmm) cc_final: 0.7359 (mtt) REVERT: G 654 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7920 (tp30) REVERT: H 50 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.6288 (p90) REVERT: I 33 ASP cc_start: 0.7787 (t0) cc_final: 0.7501 (t0) REVERT: L 660 LEU cc_start: 0.8323 (tp) cc_final: 0.8107 (tt) REVERT: M 3 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: M 60 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7977 (p) outliers start: 56 outliers final: 46 residues processed: 228 average time/residue: 0.3013 time to fit residues: 110.3773 Evaluate side-chains 228 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 145 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.167163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.161700 restraints weight = 28954.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151234 restraints weight = 58544.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.148338 restraints weight = 51955.490| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20733 Z= 0.171 Angle : 0.807 29.624 28365 Z= 0.372 Chirality : 0.050 0.524 3398 Planarity : 0.004 0.043 3456 Dihedral : 8.926 84.379 4276 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.19 % Favored : 93.64 % Rotamer: Outliers : 2.96 % Allowed : 13.38 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2454 helix: -1.34 (0.25), residues: 381 sheet: -0.05 (0.18), residues: 765 loop : -1.17 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 50 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.002 PHE F 317 TYR 0.017 0.002 TYR I 48 ARG 0.005 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 15) link_NAG-ASN : angle 9.64620 ( 45) link_ALPHA1-6 : bond 0.00463 ( 14) link_ALPHA1-6 : angle 1.80207 ( 42) link_BETA1-4 : bond 0.00653 ( 27) link_BETA1-4 : angle 1.96672 ( 81) link_ALPHA1-2 : bond 0.00848 ( 14) link_ALPHA1-2 : angle 1.86882 ( 42) link_ALPHA1-3 : bond 0.01023 ( 12) link_ALPHA1-3 : angle 1.76827 ( 36) hydrogen bonds : bond 0.03950 ( 653) hydrogen bonds : angle 5.50070 ( 1821) SS BOND : bond 0.00230 ( 45) SS BOND : angle 0.58841 ( 90) covalent geometry : bond 0.00404 (20606) covalent geometry : angle 0.69536 (28029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 348 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: G 530 MET cc_start: 0.7987 (mmm) cc_final: 0.7416 (mtt) REVERT: H 50 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.6260 (p90) REVERT: I 33 ASP cc_start: 0.7861 (t0) cc_final: 0.7527 (t0) REVERT: M 3 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7817 (pt0) outliers start: 63 outliers final: 55 residues processed: 222 average time/residue: 0.2812 time to fit residues: 100.3844 Evaluate side-chains 235 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 156 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 170 optimal weight: 0.0470 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161064 restraints weight = 28730.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.151040 restraints weight = 57335.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147517 restraints weight = 52872.742| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20733 Z= 0.186 Angle : 0.772 21.648 28365 Z= 0.368 Chirality : 0.056 1.137 3398 Planarity : 0.004 0.041 3456 Dihedral : 9.116 85.064 4276 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.99 % Favored : 93.85 % Rotamer: Outliers : 2.91 % Allowed : 14.13 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2454 helix: -1.37 (0.25), residues: 381 sheet: -0.08 (0.18), residues: 765 loop : -1.18 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 50 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.002 PHE F 317 TYR 0.016 0.002 TYR I 48 ARG 0.005 0.000 ARG L 542 Details of bonding type rmsd link_NAG-ASN : bond 0.01268 ( 15) link_NAG-ASN : angle 6.92853 ( 45) link_ALPHA1-6 : bond 0.00472 ( 14) link_ALPHA1-6 : angle 1.82852 ( 42) link_BETA1-4 : bond 0.00627 ( 27) link_BETA1-4 : angle 1.93885 ( 81) link_ALPHA1-2 : bond 0.00840 ( 14) link_ALPHA1-2 : angle 1.85358 ( 42) link_ALPHA1-3 : bond 0.01029 ( 12) link_ALPHA1-3 : angle 1.76117 ( 36) hydrogen bonds : bond 0.04070 ( 653) hydrogen bonds : angle 5.52638 ( 1821) SS BOND : bond 0.00239 ( 45) SS BOND : angle 0.61674 ( 90) covalent geometry : bond 0.00441 (20606) covalent geometry : angle 0.70746 (28029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 SER cc_start: 0.7747 (t) cc_final: 0.7482 (m) REVERT: F 348 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: H 50 TRP cc_start: 0.8185 (OUTLIER) cc_final: 0.6347 (p90) REVERT: I 33 ASP cc_start: 0.7888 (t0) cc_final: 0.7662 (t0) REVERT: M 3 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7812 (pt0) outliers start: 62 outliers final: 56 residues processed: 222 average time/residue: 0.2852 time to fit residues: 102.4641 Evaluate side-chains 234 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 200 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 171 optimal weight: 0.3980 chunk 77 optimal weight: 20.0000 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.163417 restraints weight = 28738.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153065 restraints weight = 54747.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.150395 restraints weight = 50079.273| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20733 Z= 0.140 Angle : 0.722 19.854 28365 Z= 0.343 Chirality : 0.052 0.873 3398 Planarity : 0.004 0.038 3456 Dihedral : 8.711 80.819 4276 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.58 % Rotamer: Outliers : 2.63 % Allowed : 14.51 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2454 helix: -1.12 (0.26), residues: 372 sheet: -0.09 (0.18), residues: 762 loop : -1.06 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE F 317 TYR 0.015 0.001 TYR I 48 ARG 0.005 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.01279 ( 15) link_NAG-ASN : angle 6.64009 ( 45) link_ALPHA1-6 : bond 0.00501 ( 14) link_ALPHA1-6 : angle 1.76084 ( 42) link_BETA1-4 : bond 0.00619 ( 27) link_BETA1-4 : angle 1.93086 ( 81) link_ALPHA1-2 : bond 0.00823 ( 14) link_ALPHA1-2 : angle 1.78948 ( 42) link_ALPHA1-3 : bond 0.01041 ( 12) link_ALPHA1-3 : angle 1.67734 ( 36) hydrogen bonds : bond 0.03816 ( 653) hydrogen bonds : angle 5.37212 ( 1821) SS BOND : bond 0.00203 ( 45) SS BOND : angle 0.58803 ( 90) covalent geometry : bond 0.00317 (20606) covalent geometry : angle 0.65660 (28029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9022 (mtp) cc_final: 0.8647 (mtp) REVERT: H 50 TRP cc_start: 0.8135 (OUTLIER) cc_final: 0.6343 (p90) REVERT: L 660 LEU cc_start: 0.8327 (tp) cc_final: 0.8098 (tt) REVERT: M 3 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7846 (pt0) outliers start: 56 outliers final: 51 residues processed: 220 average time/residue: 0.2825 time to fit residues: 101.7692 Evaluate side-chains 229 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 158 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.161711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155982 restraints weight = 29113.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145195 restraints weight = 59697.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141271 restraints weight = 61383.726| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 20733 Z= 0.367 Angle : 0.932 19.576 28365 Z= 0.452 Chirality : 0.060 0.913 3398 Planarity : 0.006 0.057 3456 Dihedral : 9.892 94.049 4276 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.54 % Favored : 92.26 % Rotamer: Outliers : 3.05 % Allowed : 14.13 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2454 helix: -1.88 (0.24), residues: 405 sheet: -0.19 (0.18), residues: 780 loop : -1.44 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 50 HIS 0.009 0.002 HIS H 35 PHE 0.021 0.003 PHE M 64 TYR 0.021 0.003 TYR M 106 ARG 0.008 0.001 ARG L 542 Details of bonding type rmsd link_NAG-ASN : bond 0.01508 ( 15) link_NAG-ASN : angle 6.81100 ( 45) link_ALPHA1-6 : bond 0.00497 ( 14) link_ALPHA1-6 : angle 1.95067 ( 42) link_BETA1-4 : bond 0.00754 ( 27) link_BETA1-4 : angle 2.35418 ( 81) link_ALPHA1-2 : bond 0.00878 ( 14) link_ALPHA1-2 : angle 1.94328 ( 42) link_ALPHA1-3 : bond 0.01032 ( 12) link_ALPHA1-3 : angle 1.95679 ( 36) hydrogen bonds : bond 0.05037 ( 653) hydrogen bonds : angle 6.05098 ( 1821) SS BOND : bond 0.00405 ( 45) SS BOND : angle 0.87208 ( 90) covalent geometry : bond 0.00902 (20606) covalent geometry : angle 0.87753 (28029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5642.05 seconds wall clock time: 101 minutes 20.69 seconds (6080.69 seconds total)