Starting phenix.real_space_refine on Tue May 20 17:47:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb5_40291/05_2025/8sb5_40291_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb5_40291/05_2025/8sb5_40291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sb5_40291/05_2025/8sb5_40291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb5_40291/05_2025/8sb5_40291.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb5_40291/05_2025/8sb5_40291_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb5_40291/05_2025/8sb5_40291_neut.cif" } resolution = 3.9 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= -0.000 sd= 1.000 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 12620 2.51 5 N 3338 2.21 5 O 4106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20205 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3607 Classifications: {'peptide': 461} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 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: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} 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: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} 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: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" 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: "J" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 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: "W" 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: "X" 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 Time building chain proxies: 12.23, per 1000 atoms: 0.61 Number of scatterers: 20205 At special positions: 0 Unit cell: (156, 154.96, 134.16, 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 4106 8.00 N 3338 7.00 C 12620 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 321 " - pdb=" SG CYS D 331 " 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=2.04 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 252 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS I 321 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " distance=2.03 Simple disulfide: pdb=" SG CYS N 321 " - pdb=" SG CYS N 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN J 10 " - " MAN J 11 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " " MAN V 10 " - " MAN V 11 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 10 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 10 " 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 R 2 " - " BMA R 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 6.07 Conformation dependent library (CDL) restraints added in 2.6 seconds 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 46 sheets defined 20.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.472A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.957A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.494A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.562A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.285A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.760A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 311 through 315 removed outlier: 3.700A pdb=" N GLU D 315 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.472A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.674A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 4.453A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 596 Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.359A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 3.744A pdb=" N ILE G 642 " --> pdb=" O TYR G 638 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU G 647 " --> pdb=" O TYR G 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 311 through 315 Processing helix chain 'K' and resid 57 through 61 Processing helix chain 'K' and resid 68 through 72 Processing helix chain 'K' and resid 98 through 117 removed outlier: 4.522A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 387 through 390 Processing helix chain 'K' and resid 475 through 481 removed outlier: 3.712A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 536 through 543 removed outlier: 4.471A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.542A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.313A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 3.768A pdb=" N ILE L 642 " --> pdb=" O TYR L 638 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU L 647 " --> pdb=" O TYR L 643 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 311 through 315 removed outlier: 3.615A pdb=" N GLU N 315 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.599A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 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 176 removed outlier: 4.312A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.746A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.185A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.450A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.505A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.811A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP C 50 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 98 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS C 116 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.811A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP C 50 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 253 Processing sheet with id=AB5, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.438A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR D 281 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 265 " --> pdb=" O TYR D 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.438A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR D 281 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 265 " --> pdb=" O TYR D 281 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 499 Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.241A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.751A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS F 218 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 176 removed outlier: 4.581A pdb=" N ASN F 156 " --> pdb=" O SER F 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.775A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.186A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 359 " --> pdb=" O TYR F 395 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.457A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.735A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 93 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.735A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 93 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 248 through 253 Processing sheet with id=AD2, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.478A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR I 281 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 265 " --> pdb=" O TYR I 281 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.478A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR I 281 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 265 " --> pdb=" O TYR I 281 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 499 Processing sheet with id=AD5, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.590A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU K 84 " --> pdb=" O THR K 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 55 through 56 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 176 removed outlier: 4.361A pdb=" N ASN K 156 " --> pdb=" O SER K 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 259 through 261 removed outlier: 3.787A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.215A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 3.787A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.215A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.409A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE K 359 " --> pdb=" O TYR K 395 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 423 through 424 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 58 through 60 removed outlier: 3.905A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP M 50 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS M 116 " --> pdb=" O THR M 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.905A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP M 50 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 248 through 253 Processing sheet with id=AE9, first strand: chain 'N' and resid 277 through 281 removed outlier: 6.593A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 277 through 281 removed outlier: 6.593A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 1920 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: 7.38 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4671 1.33 - 1.45: 4828 1.45 - 1.58: 10932 1.58 - 1.70: 10 1.70 - 1.82: 192 Bond restraints: 20633 Sorted by residual: bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.607 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 BMA T 3 " pdb=" C2 BMA T 3 " ideal model delta sigma weight residual 1.519 1.604 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.601 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 MAN V 9 " pdb=" C2 MAN V 9 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.472 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 20628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 26971 2.20 - 4.40: 847 4.40 - 6.60: 191 6.60 - 8.80: 45 8.80 - 11.00: 10 Bond angle restraints: 28064 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.70 -11.00 1.80e+00 3.09e-01 3.73e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 132.61 -10.91 1.80e+00 3.09e-01 3.67e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.60 -10.90 1.80e+00 3.09e-01 3.67e+01 angle pdb=" C ASN F 403 " pdb=" N SER F 404 " pdb=" CA SER F 404 " ideal model delta sigma weight residual 121.70 130.99 -9.29 1.80e+00 3.09e-01 2.66e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 130.87 -9.17 1.80e+00 3.09e-01 2.60e+01 ... (remaining 28059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 12348 22.74 - 45.48: 661 45.48 - 68.22: 89 68.22 - 90.96: 99 90.96 - 113.69: 48 Dihedral angle restraints: 13245 sinusoidal: 6091 harmonic: 7154 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -149.71 63.71 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS K 119 " pdb=" SG CYS K 119 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual -86.00 -148.18 62.18 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -146.87 60.87 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 13242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2785 0.066 - 0.131: 492 0.131 - 0.197: 83 0.197 - 0.262: 3 0.262 - 0.328: 11 Chirality restraints: 3374 Sorted by residual: chirality pdb=" CA THR A 123 " pdb=" N THR A 123 " pdb=" C THR A 123 " pdb=" CB THR A 123 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3371 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 84 " -0.364 9.50e-02 1.11e+02 1.63e-01 1.78e+01 pdb=" NE ARG M 84 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG M 84 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG M 84 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG M 84 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 596 " 0.028 2.00e-02 2.50e+03 1.91e-02 9.16e+00 pdb=" CG TRP L 596 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP L 596 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP L 596 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP L 596 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 596 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 596 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 596 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 596 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 596 " 0.024 2.00e-02 2.50e+03 1.69e-02 7.12e+00 pdb=" CG TRP B 596 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 596 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 596 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 596 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 596 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 596 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 596 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 596 " 0.001 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 386 2.66 - 3.22: 19495 3.22 - 3.78: 29478 3.78 - 4.34: 41440 4.34 - 4.90: 69021 Nonbonded interactions: 159820 Sorted by model distance: nonbonded pdb=" OG1 THR M 28 " pdb=" OD2 ASP M 31 " model vdw 2.103 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN K 463 " pdb=" OG1 THR K 465 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR G 529 " pdb=" O ASP G 624 " model vdw 2.143 3.040 nonbonded pdb=" OG SER I 295 " pdb=" OG1 THR I 306 " model vdw 2.160 3.040 ... (remaining 159815 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' and (resid 32 through 443 or resid 445 through 505)) selection = (chain 'K' and (resid 32 through 443 or resid 445 through 505)) } 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 'E' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 47.500 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.140 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 0.114 20752 Z= 0.286 Angle : 1.058 14.732 28376 Z= 0.521 Chirality : 0.055 0.328 3374 Planarity : 0.006 0.163 3469 Dihedral : 17.058 113.694 8534 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.20 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.51 (0.16), residues: 2463 helix: -0.60 (0.26), residues: 399 sheet: -0.72 (0.20), residues: 614 loop : -1.24 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP L 596 HIS 0.012 0.002 HIS A 374 PHE 0.010 0.001 PHE A 376 TYR 0.032 0.003 TYR K 395 ARG 0.021 0.001 ARG M 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 12) link_NAG-ASN : angle 2.58635 ( 36) link_ALPHA1-6 : bond 0.00514 ( 6) link_ALPHA1-6 : angle 2.84282 ( 18) link_BETA1-4 : bond 0.01158 ( 24) link_BETA1-4 : angle 4.83187 ( 72) link_ALPHA1-2 : bond 0.01397 ( 20) link_ALPHA1-2 : angle 4.71896 ( 60) link_ALPHA1-3 : bond 0.00937 ( 12) link_ALPHA1-3 : angle 3.09838 ( 36) hydrogen bonds : bond 0.22082 ( 677) hydrogen bonds : angle 9.05040 ( 1920) SS BOND : bond 0.00318 ( 45) SS BOND : angle 1.45326 ( 90) covalent geometry : bond 0.00602 (20633) covalent geometry : angle 0.99624 (28064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 ILE cc_start: 0.8929 (mm) cc_final: 0.8615 (mm) REVERT: B 535 MET cc_start: 0.7560 (mmm) cc_final: 0.7321 (mmt) REVERT: D 271 HIS cc_start: 0.6171 (m-70) cc_final: 0.5957 (m-70) REVERT: H 27 TYR cc_start: 0.4325 (m-10) cc_final: 0.3870 (m-80) REVERT: M 6 GLN cc_start: 0.7203 (mt0) cc_final: 0.6878 (mt0) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.3065 time to fit residues: 175.8151 Evaluate side-chains 287 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.0470 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 117 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 374 HIS C 43 GLN C 116 HIS F 289 HIS F 374 HIS G 577 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS N 270 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157636 restraints weight = 28170.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150578 restraints weight = 38761.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.150160 restraints weight = 34261.408| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20752 Z= 0.173 Angle : 0.803 13.511 28376 Z= 0.400 Chirality : 0.048 0.235 3374 Planarity : 0.004 0.055 3469 Dihedral : 13.861 90.136 4119 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.13 % Rotamer: Outliers : 0.93 % Allowed : 7.32 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -1.26 (0.17), residues: 2463 helix: 0.02 (0.27), residues: 372 sheet: -0.64 (0.20), residues: 645 loop : -1.15 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 35 HIS 0.005 0.001 HIS C 35 PHE 0.027 0.002 PHE A 391 TYR 0.021 0.002 TYR D 281 ARG 0.008 0.001 ARG L 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 12) link_NAG-ASN : angle 2.15150 ( 36) link_ALPHA1-6 : bond 0.00579 ( 6) link_ALPHA1-6 : angle 1.87446 ( 18) link_BETA1-4 : bond 0.01380 ( 24) link_BETA1-4 : angle 3.47634 ( 72) link_ALPHA1-2 : bond 0.01197 ( 20) link_ALPHA1-2 : angle 3.33953 ( 60) link_ALPHA1-3 : bond 0.01243 ( 12) link_ALPHA1-3 : angle 1.56846 ( 36) hydrogen bonds : bond 0.05335 ( 677) hydrogen bonds : angle 6.39162 ( 1920) SS BOND : bond 0.00360 ( 45) SS BOND : angle 0.97233 ( 90) covalent geometry : bond 0.00376 (20633) covalent geometry : angle 0.76315 (28064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.8225 (t-170) REVERT: B 542 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6558 (ttm170) REVERT: B 575 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7093 (tm-30) REVERT: F 374 HIS cc_start: 0.8975 (OUTLIER) cc_final: 0.8683 (t-170) REVERT: K 180 ASP cc_start: 0.8292 (m-30) cc_final: 0.8075 (t0) REVERT: K 500 ARG cc_start: 0.7597 (ptp-170) cc_final: 0.7352 (ptp-170) outliers start: 20 outliers final: 11 residues processed: 315 average time/residue: 0.3144 time to fit residues: 152.7527 Evaluate side-chains 268 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 55 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 229 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 258 GLN B 651 ASN F 229 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS K 229 ASN K 258 GLN K 374 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150555 restraints weight = 28055.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149995 restraints weight = 27432.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149765 restraints weight = 28945.850| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20752 Z= 0.168 Angle : 0.760 12.729 28376 Z= 0.378 Chirality : 0.047 0.221 3374 Planarity : 0.005 0.076 3469 Dihedral : 12.013 86.024 4119 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.55 % Favored : 95.25 % Rotamer: Outliers : 1.77 % Allowed : 9.56 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -1.10 (0.17), residues: 2463 helix: 0.23 (0.27), residues: 372 sheet: -0.52 (0.20), residues: 642 loop : -1.08 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 35 HIS 0.008 0.001 HIS K 289 PHE 0.018 0.002 PHE A 391 TYR 0.030 0.002 TYR A 486 ARG 0.010 0.001 ARG L 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 12) link_NAG-ASN : angle 2.12461 ( 36) link_ALPHA1-6 : bond 0.00428 ( 6) link_ALPHA1-6 : angle 1.82001 ( 18) link_BETA1-4 : bond 0.01278 ( 24) link_BETA1-4 : angle 3.25442 ( 72) link_ALPHA1-2 : bond 0.01061 ( 20) link_ALPHA1-2 : angle 2.86308 ( 60) link_ALPHA1-3 : bond 0.01141 ( 12) link_ALPHA1-3 : angle 1.52083 ( 36) hydrogen bonds : bond 0.04481 ( 677) hydrogen bonds : angle 5.70161 ( 1920) SS BOND : bond 0.00435 ( 45) SS BOND : angle 1.58957 ( 90) covalent geometry : bond 0.00380 (20633) covalent geometry : angle 0.72165 (28064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7828 (p0) cc_final: 0.7416 (t0) REVERT: G 542 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7549 (ttm170) REVERT: H 81 MET cc_start: 0.7622 (tmm) cc_final: 0.7075 (tmm) REVERT: K 374 HIS cc_start: 0.8876 (OUTLIER) cc_final: 0.8593 (t-170) REVERT: M 81 MET cc_start: 0.7588 (tmm) cc_final: 0.7279 (tmm) outliers start: 38 outliers final: 23 residues processed: 291 average time/residue: 0.3037 time to fit residues: 138.8657 Evaluate side-chains 266 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 51 MET Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 137 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 ASN L 616 ASN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.157003 restraints weight = 28343.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.150156 restraints weight = 36845.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148777 restraints weight = 33840.185| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20752 Z= 0.150 Angle : 0.724 13.508 28376 Z= 0.361 Chirality : 0.046 0.219 3374 Planarity : 0.004 0.059 3469 Dihedral : 10.574 80.763 4119 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.67 % Favored : 95.13 % Rotamer: Outliers : 2.47 % Allowed : 10.96 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.93 (0.17), residues: 2463 helix: 0.53 (0.27), residues: 375 sheet: -0.43 (0.20), residues: 642 loop : -1.02 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 571 HIS 0.015 0.001 HIS K 374 PHE 0.011 0.002 PHE I 323 TYR 0.020 0.002 TYR N 319 ARG 0.005 0.000 ARG L 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 12) link_NAG-ASN : angle 1.98887 ( 36) link_ALPHA1-6 : bond 0.00418 ( 6) link_ALPHA1-6 : angle 1.80754 ( 18) link_BETA1-4 : bond 0.01156 ( 24) link_BETA1-4 : angle 3.04030 ( 72) link_ALPHA1-2 : bond 0.00960 ( 20) link_ALPHA1-2 : angle 2.64820 ( 60) link_ALPHA1-3 : bond 0.01129 ( 12) link_ALPHA1-3 : angle 1.49487 ( 36) hydrogen bonds : bond 0.03988 ( 677) hydrogen bonds : angle 5.37698 ( 1920) SS BOND : bond 0.00612 ( 45) SS BOND : angle 1.52634 ( 90) covalent geometry : bond 0.00337 (20633) covalent geometry : angle 0.68871 (28064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7841 (p0) cc_final: 0.7449 (t0) REVERT: A 377 ASN cc_start: 0.8397 (t0) cc_final: 0.8186 (t0) REVERT: A 475 MET cc_start: 0.5826 (mmt) cc_final: 0.5351 (tpt) REVERT: B 542 ARG cc_start: 0.7421 (ttm170) cc_final: 0.6819 (ttm170) REVERT: D 301 ASN cc_start: 0.5996 (t0) cc_final: 0.5783 (t0) REVERT: F 99 ASP cc_start: 0.7773 (p0) cc_final: 0.7496 (t0) REVERT: G 542 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7512 (ttm170) REVERT: K 423 ILE cc_start: 0.9190 (mm) cc_final: 0.8927 (mm) REVERT: K 481 SER cc_start: 0.9215 (p) cc_final: 0.8907 (t) REVERT: K 500 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.7406 (ptp-170) REVERT: L 543 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7007 (p0) REVERT: M 81 MET cc_start: 0.7575 (tmm) cc_final: 0.7180 (tmm) outliers start: 53 outliers final: 22 residues processed: 302 average time/residue: 0.2898 time to fit residues: 138.9532 Evaluate side-chains 265 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 543 ASN Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 113 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 138 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 HIS ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 616 ASN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161236 restraints weight = 31122.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159743 restraints weight = 42630.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159339 restraints weight = 45304.091| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20752 Z= 0.153 Angle : 0.716 12.774 28376 Z= 0.356 Chirality : 0.046 0.231 3374 Planarity : 0.004 0.062 3469 Dihedral : 9.967 78.143 4119 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.59 % Favored : 95.21 % Rotamer: Outliers : 2.10 % Allowed : 11.75 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -0.83 (0.17), residues: 2463 helix: 0.76 (0.27), residues: 375 sheet: -0.43 (0.20), residues: 652 loop : -0.96 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 571 HIS 0.005 0.001 HIS C 35 PHE 0.011 0.001 PHE D 323 TYR 0.025 0.002 TYR F 486 ARG 0.004 0.000 ARG L 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 12) link_NAG-ASN : angle 1.95195 ( 36) link_ALPHA1-6 : bond 0.00426 ( 6) link_ALPHA1-6 : angle 1.78123 ( 18) link_BETA1-4 : bond 0.01164 ( 24) link_BETA1-4 : angle 2.98707 ( 72) link_ALPHA1-2 : bond 0.00912 ( 20) link_ALPHA1-2 : angle 2.51072 ( 60) link_ALPHA1-3 : bond 0.01095 ( 12) link_ALPHA1-3 : angle 1.47726 ( 36) hydrogen bonds : bond 0.03821 ( 677) hydrogen bonds : angle 5.20646 ( 1920) SS BOND : bond 0.00596 ( 45) SS BOND : angle 1.38938 ( 90) covalent geometry : bond 0.00346 (20633) covalent geometry : angle 0.68314 (28064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7895 (p0) cc_final: 0.7441 (t0) REVERT: A 377 ASN cc_start: 0.8446 (t0) cc_final: 0.8227 (t0) REVERT: A 475 MET cc_start: 0.5754 (mmt) cc_final: 0.5426 (tpt) REVERT: B 542 ARG cc_start: 0.7383 (ttm170) cc_final: 0.6826 (ttm170) REVERT: D 301 ASN cc_start: 0.5806 (t0) cc_final: 0.5556 (t0) REVERT: F 99 ASP cc_start: 0.7798 (p0) cc_final: 0.7519 (t0) REVERT: G 542 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7566 (ttm170) REVERT: K 481 SER cc_start: 0.9230 (p) cc_final: 0.8988 (t) REVERT: L 542 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7569 (mtp-110) outliers start: 45 outliers final: 27 residues processed: 292 average time/residue: 0.3029 time to fit residues: 137.7768 Evaluate side-chains 263 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 GLN ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.175434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.160281 restraints weight = 30966.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.158515 restraints weight = 50072.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158363 restraints weight = 49346.853| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20752 Z= 0.179 Angle : 0.730 12.719 28376 Z= 0.364 Chirality : 0.046 0.218 3374 Planarity : 0.004 0.057 3469 Dihedral : 9.717 77.861 4119 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.64 % Favored : 94.15 % Rotamer: Outliers : 2.66 % Allowed : 11.99 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -0.77 (0.17), residues: 2463 helix: 0.93 (0.27), residues: 375 sheet: -0.43 (0.20), residues: 657 loop : -0.93 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 614 HIS 0.007 0.001 HIS C 35 PHE 0.016 0.002 PHE I 323 TYR 0.027 0.002 TYR K 486 ARG 0.005 0.000 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 12) link_NAG-ASN : angle 2.08035 ( 36) link_ALPHA1-6 : bond 0.00426 ( 6) link_ALPHA1-6 : angle 1.75620 ( 18) link_BETA1-4 : bond 0.01193 ( 24) link_BETA1-4 : angle 2.95286 ( 72) link_ALPHA1-2 : bond 0.00881 ( 20) link_ALPHA1-2 : angle 2.39083 ( 60) link_ALPHA1-3 : bond 0.01059 ( 12) link_ALPHA1-3 : angle 1.49149 ( 36) hydrogen bonds : bond 0.03825 ( 677) hydrogen bonds : angle 5.22009 ( 1920) SS BOND : bond 0.00627 ( 45) SS BOND : angle 1.37559 ( 90) covalent geometry : bond 0.00409 (20633) covalent geometry : angle 0.69886 (28064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7919 (p0) cc_final: 0.7490 (t0) REVERT: B 542 ARG cc_start: 0.7475 (ttm170) cc_final: 0.6698 (ttm170) REVERT: F 99 ASP cc_start: 0.7760 (p0) cc_final: 0.7468 (t0) REVERT: F 298 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8415 (ttp-170) REVERT: G 542 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7604 (ttm170) REVERT: H 48 MET cc_start: 0.7385 (mtp) cc_final: 0.7111 (mtm) REVERT: K 481 SER cc_start: 0.9288 (p) cc_final: 0.9044 (t) REVERT: K 500 ARG cc_start: 0.7549 (ptp-170) cc_final: 0.7325 (ptp-170) REVERT: L 542 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7447 (mtp-110) REVERT: M 81 MET cc_start: 0.7306 (tmm) cc_final: 0.7056 (tmm) outliers start: 57 outliers final: 38 residues processed: 298 average time/residue: 0.3133 time to fit residues: 144.7553 Evaluate side-chains 276 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 5 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 200 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 213 optimal weight: 0.4980 chunk 237 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 616 ASN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159284 restraints weight = 30810.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157886 restraints weight = 47878.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157563 restraints weight = 48379.851| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20752 Z= 0.180 Angle : 0.732 13.076 28376 Z= 0.364 Chirality : 0.046 0.217 3374 Planarity : 0.004 0.056 3469 Dihedral : 9.489 77.155 4119 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.56 % Favored : 94.23 % Rotamer: Outliers : 2.66 % Allowed : 13.15 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -0.73 (0.17), residues: 2463 helix: 1.07 (0.27), residues: 375 sheet: -0.37 (0.20), residues: 645 loop : -0.96 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 596 HIS 0.007 0.001 HIS C 35 PHE 0.014 0.002 PHE I 323 TYR 0.017 0.002 TYR I 319 ARG 0.008 0.000 ARG L 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 12) link_NAG-ASN : angle 2.03408 ( 36) link_ALPHA1-6 : bond 0.00417 ( 6) link_ALPHA1-6 : angle 1.75970 ( 18) link_BETA1-4 : bond 0.01131 ( 24) link_BETA1-4 : angle 2.90960 ( 72) link_ALPHA1-2 : bond 0.00866 ( 20) link_ALPHA1-2 : angle 2.30890 ( 60) link_ALPHA1-3 : bond 0.01018 ( 12) link_ALPHA1-3 : angle 1.45109 ( 36) hydrogen bonds : bond 0.03764 ( 677) hydrogen bonds : angle 5.19075 ( 1920) SS BOND : bond 0.00569 ( 45) SS BOND : angle 1.27434 ( 90) covalent geometry : bond 0.00415 (20633) covalent geometry : angle 0.70237 (28064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7916 (p0) cc_final: 0.7457 (t0) REVERT: B 542 ARG cc_start: 0.7463 (ttm170) cc_final: 0.6712 (ttm170) REVERT: C 47 TRP cc_start: 0.8132 (t60) cc_final: 0.7747 (t60) REVERT: F 99 ASP cc_start: 0.7798 (p0) cc_final: 0.7496 (t0) REVERT: F 298 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: F 374 HIS cc_start: 0.9169 (OUTLIER) cc_final: 0.8351 (t-90) REVERT: F 481 SER cc_start: 0.9289 (p) cc_final: 0.9064 (t) REVERT: G 542 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7592 (ttm170) REVERT: H 47 TRP cc_start: 0.8083 (t60) cc_final: 0.7538 (t60) REVERT: K 374 HIS cc_start: 0.8963 (OUTLIER) cc_final: 0.8350 (t-170) outliers start: 57 outliers final: 42 residues processed: 298 average time/residue: 0.3123 time to fit residues: 144.4444 Evaluate side-chains 290 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 304 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 179 optimal weight: 0.0770 chunk 192 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160986 restraints weight = 30907.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159546 restraints weight = 41182.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159016 restraints weight = 41749.684| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20752 Z= 0.142 Angle : 0.701 12.553 28376 Z= 0.350 Chirality : 0.045 0.207 3374 Planarity : 0.004 0.055 3469 Dihedral : 8.964 73.614 4119 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.99 % Favored : 94.80 % Rotamer: Outliers : 2.29 % Allowed : 14.04 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -0.58 (0.17), residues: 2463 helix: 1.29 (0.27), residues: 372 sheet: -0.24 (0.20), residues: 631 loop : -0.90 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 596 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE K 210 TYR 0.021 0.002 TYR I 319 ARG 0.003 0.000 ARG L 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 12) link_NAG-ASN : angle 1.78474 ( 36) link_ALPHA1-6 : bond 0.00443 ( 6) link_ALPHA1-6 : angle 1.69550 ( 18) link_BETA1-4 : bond 0.01090 ( 24) link_BETA1-4 : angle 2.77060 ( 72) link_ALPHA1-2 : bond 0.00832 ( 20) link_ALPHA1-2 : angle 2.23010 ( 60) link_ALPHA1-3 : bond 0.01033 ( 12) link_ALPHA1-3 : angle 1.37552 ( 36) hydrogen bonds : bond 0.03616 ( 677) hydrogen bonds : angle 5.09155 ( 1920) SS BOND : bond 0.00522 ( 45) SS BOND : angle 1.37481 ( 90) covalent geometry : bond 0.00317 (20633) covalent geometry : angle 0.67237 (28064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7911 (p0) cc_final: 0.7453 (t0) REVERT: B 542 ARG cc_start: 0.7384 (ttm170) cc_final: 0.6678 (ttm170) REVERT: C 47 TRP cc_start: 0.8186 (t60) cc_final: 0.7938 (t60) REVERT: F 99 ASP cc_start: 0.7766 (p0) cc_final: 0.7490 (t0) REVERT: F 298 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8375 (ttp-170) REVERT: F 374 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8741 (t-170) REVERT: F 481 SER cc_start: 0.9264 (p) cc_final: 0.9044 (t) REVERT: G 542 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7484 (ttm170) REVERT: H 47 TRP cc_start: 0.8035 (t60) cc_final: 0.7400 (t60) REVERT: M 47 TRP cc_start: 0.8108 (t60) cc_final: 0.7293 (t60) outliers start: 49 outliers final: 41 residues processed: 300 average time/residue: 0.3038 time to fit residues: 141.7622 Evaluate side-chains 296 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 304 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 6 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 207 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN N 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.166643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155180 restraints weight = 28180.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154658 restraints weight = 45004.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154628 restraints weight = 43701.261| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20752 Z= 0.171 Angle : 0.714 12.660 28376 Z= 0.357 Chirality : 0.046 0.211 3374 Planarity : 0.004 0.053 3469 Dihedral : 8.740 73.770 4119 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.48 % Favored : 94.32 % Rotamer: Outliers : 2.66 % Allowed : 14.09 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -0.58 (0.17), residues: 2463 helix: 1.37 (0.27), residues: 369 sheet: -0.14 (0.21), residues: 616 loop : -0.96 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 596 HIS 0.023 0.002 HIS F 374 PHE 0.013 0.002 PHE I 323 TYR 0.035 0.002 TYR I 319 ARG 0.003 0.000 ARG L 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 12) link_NAG-ASN : angle 1.95071 ( 36) link_ALPHA1-6 : bond 0.00472 ( 6) link_ALPHA1-6 : angle 1.68099 ( 18) link_BETA1-4 : bond 0.01071 ( 24) link_BETA1-4 : angle 2.77397 ( 72) link_ALPHA1-2 : bond 0.00837 ( 20) link_ALPHA1-2 : angle 2.18831 ( 60) link_ALPHA1-3 : bond 0.00989 ( 12) link_ALPHA1-3 : angle 1.39231 ( 36) hydrogen bonds : bond 0.03671 ( 677) hydrogen bonds : angle 5.10822 ( 1920) SS BOND : bond 0.00563 ( 45) SS BOND : angle 1.31873 ( 90) covalent geometry : bond 0.00394 (20633) covalent geometry : angle 0.68592 (28064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 254 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7534 (ttm170) cc_final: 0.6826 (ttm170) REVERT: C 47 TRP cc_start: 0.8169 (t60) cc_final: 0.7927 (t60) REVERT: F 298 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8222 (ttp-170) REVERT: F 481 SER cc_start: 0.9247 (p) cc_final: 0.9030 (t) REVERT: G 542 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7565 (ttm170) REVERT: H 47 TRP cc_start: 0.8082 (t60) cc_final: 0.7416 (t60) REVERT: M 47 TRP cc_start: 0.8170 (t60) cc_final: 0.7381 (t60) outliers start: 57 outliers final: 47 residues processed: 295 average time/residue: 0.3217 time to fit residues: 146.6690 Evaluate side-chains 291 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 107 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 71 optimal weight: 0.0000 chunk 208 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.158225 restraints weight = 28083.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157472 restraints weight = 43968.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.157029 restraints weight = 45006.360| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20752 Z= 0.132 Angle : 0.683 12.548 28376 Z= 0.341 Chirality : 0.045 0.211 3374 Planarity : 0.004 0.052 3469 Dihedral : 8.090 69.037 4119 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.09 % Rotamer: Outliers : 2.05 % Allowed : 14.88 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -0.49 (0.17), residues: 2463 helix: 1.47 (0.28), residues: 369 sheet: -0.06 (0.21), residues: 614 loop : -0.91 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 596 HIS 0.006 0.001 HIS A 374 PHE 0.010 0.001 PHE K 210 TYR 0.034 0.002 TYR I 319 ARG 0.008 0.000 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 12) link_NAG-ASN : angle 1.65632 ( 36) link_ALPHA1-6 : bond 0.00532 ( 6) link_ALPHA1-6 : angle 1.61574 ( 18) link_BETA1-4 : bond 0.00986 ( 24) link_BETA1-4 : angle 2.57672 ( 72) link_ALPHA1-2 : bond 0.00798 ( 20) link_ALPHA1-2 : angle 2.09635 ( 60) link_ALPHA1-3 : bond 0.01018 ( 12) link_ALPHA1-3 : angle 1.31055 ( 36) hydrogen bonds : bond 0.03453 ( 677) hydrogen bonds : angle 4.94564 ( 1920) SS BOND : bond 0.00506 ( 45) SS BOND : angle 1.17273 ( 90) covalent geometry : bond 0.00292 (20633) covalent geometry : angle 0.65832 (28064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.6740 (OUTLIER) cc_final: 0.6477 (t-100) REVERT: B 542 ARG cc_start: 0.7458 (ttm170) cc_final: 0.6611 (ttm170) REVERT: F 298 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8275 (ttp-170) REVERT: F 481 SER cc_start: 0.9218 (p) cc_final: 0.8994 (t) REVERT: G 542 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7229 (ttm170) REVERT: H 47 TRP cc_start: 0.8141 (t60) cc_final: 0.7391 (t60) REVERT: M 47 TRP cc_start: 0.8152 (t60) cc_final: 0.7811 (t60) REVERT: N 304 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7263 (p) outliers start: 44 outliers final: 35 residues processed: 288 average time/residue: 0.3182 time to fit residues: 142.1469 Evaluate side-chains 288 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 101 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN F 374 HIS G 540 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 271 HIS ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 GLN K 374 HIS ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146939 restraints weight = 28362.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.146379 restraints weight = 28849.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146103 restraints weight = 30519.168| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20752 Z= 0.191 Angle : 0.731 12.670 28376 Z= 0.366 Chirality : 0.047 0.241 3374 Planarity : 0.004 0.053 3469 Dihedral : 8.132 70.249 4119 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.46 % Favored : 93.38 % Rotamer: Outliers : 2.19 % Allowed : 14.88 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % 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: -0.55 (0.17), residues: 2463 helix: 1.35 (0.27), residues: 372 sheet: -0.10 (0.21), residues: 618 loop : -0.94 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 596 HIS 0.007 0.001 HIS C 35 PHE 0.014 0.002 PHE I 323 TYR 0.031 0.002 TYR I 319 ARG 0.006 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 12) link_NAG-ASN : angle 2.07600 ( 36) link_ALPHA1-6 : bond 0.00631 ( 6) link_ALPHA1-6 : angle 1.57524 ( 18) link_BETA1-4 : bond 0.00961 ( 24) link_BETA1-4 : angle 2.66022 ( 72) link_ALPHA1-2 : bond 0.00829 ( 20) link_ALPHA1-2 : angle 2.08728 ( 60) link_ALPHA1-3 : bond 0.00961 ( 12) link_ALPHA1-3 : angle 1.36953 ( 36) hydrogen bonds : bond 0.03705 ( 677) hydrogen bonds : angle 5.09989 ( 1920) SS BOND : bond 0.00627 ( 45) SS BOND : angle 1.25528 ( 90) covalent geometry : bond 0.00445 (20633) covalent geometry : angle 0.70602 (28064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5946.57 seconds wall clock time: 105 minutes 39.44 seconds (6339.44 seconds total)