Starting phenix.real_space_refine on Sun Aug 24 13:32:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3v_29710/08_2025/8g3v_29710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3v_29710/08_2025/8g3v_29710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3v_29710/08_2025/8g3v_29710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3v_29710/08_2025/8g3v_29710.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3v_29710/08_2025/8g3v_29710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3v_29710/08_2025/8g3v_29710.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12484 2.51 5 N 3416 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20045 Number of models: 1 Model: "" Number of chains: 28 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "A" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.03, per 1000 atoms: 0.20 Number of scatterers: 20045 At special positions: 0 Unit cell: (131.97, 131.97, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4024 8.00 N 3416 7.00 C 12484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.06 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.08 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.11 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.11 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.10 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.11 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.11 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.10 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.10 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.05 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.06 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.07 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.03 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 230 " distance=2.08 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 237 " distance=2.11 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.11 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.10 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.10 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.15 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.06 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.07 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.08 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.11 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.11 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.10 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.15 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.06 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 F 4 " - " MAN F 5 " " MAN Q 4 " - " MAN Q 5 " " MAN T 4 " - " MAN T 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA W 3 " - " MAN W 4 " " MAN W 6 " - " MAN W 7 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " MAN F 6 " - " MAN F 8 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 6 " - " MAN Q 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA W 3 " - " MAN W 6 " " MAN W 6 " - " MAN W 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN G 86 " " NAG F 1 " - " ASN G 200 " " NAG G1101 " - " ASN G 146 " " NAG G1102 " - " ASN G 367 " " NAG H1101 " - " ASN H 146 " " NAG H1102 " - " ASN H 367 " " NAG I1101 " - " ASN I 146 " " NAG I1102 " - " ASN I 367 " " NAG J1101 " - " ASN J 146 " " NAG J1102 " - " ASN J 367 " " NAG K 1 " - " ASN G 234 " " NAG P 1 " - " ASN H 86 " " NAG Q 1 " - " ASN H 200 " " NAG R 1 " - " ASN H 234 " " NAG S 1 " - " ASN I 86 " " NAG T 1 " - " ASN I 200 " " NAG U 1 " - " ASN I 234 " " NAG V 1 " - " ASN J 86 " " NAG W 1 " - " ASN J 200 " " NAG X 1 " - " ASN J 234 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 558.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.690A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.560A pdb=" N LYS A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.691A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.558A pdb=" N LYS B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.659A pdb=" N PHE M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.689A pdb=" N ASN I 146 " --> pdb=" O VAL I 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.679A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.802A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.796A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.116A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 213 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.527A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.082A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.497A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.487A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.241A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.249A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE A 117 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER L 67 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.474A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.804A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.797A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 213 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.085A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.500A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.525A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.252A pdb=" N LEU B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE B 117 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER M 67 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY I 96 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL I 445 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS I 102 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE I 443 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 115 through 124 removed outlier: 4.795A pdb=" N TRP I 115 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR I 138 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR I 117 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN I 136 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU I 119 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU I 134 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS I 172 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 179 through 184 removed outlier: 4.114A pdb=" N ASP I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP I 213 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU I 258 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 276 through 283 removed outlier: 5.384A pdb=" N GLU I 277 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG I 292 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 353 through 356 removed outlier: 7.093A pdb=" N ASP I 402 " --> pdb=" O GLY I 373 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N GLU I 375 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ARG I 400 " --> pdb=" O GLU I 375 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N PHE I 377 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 13.491A pdb=" N VAL I 398 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N VAL I 379 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL I 396 " --> pdb=" O VAL I 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.261A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE C 117 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER N 67 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.476A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.119A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP J 213 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.525A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.383A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 356 removed outlier: 7.092A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.259A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE D 117 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AF2, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.850A pdb=" N GLN O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER O 67 " --> pdb=" O GLN O 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.477A pdb=" N LEU O 33 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3703 1.32 - 1.45: 5439 1.45 - 1.57: 11206 1.57 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20492 Sorted by residual: bond pdb=" N VAL O 58 " pdb=" CA VAL O 58 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.00e+01 bond pdb=" CA SER J 457 " pdb=" CB SER J 457 " ideal model delta sigma weight residual 1.534 1.460 0.074 1.72e-02 3.38e+03 1.85e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.534 1.463 0.070 1.72e-02 3.38e+03 1.67e+01 bond pdb=" N VAL G 165 " pdb=" CA VAL G 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 bond pdb=" N VAL I 165 " pdb=" CA VAL I 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 ... (remaining 20487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 24137 2.38 - 4.77: 3467 4.77 - 7.15: 203 7.15 - 9.53: 13 9.53 - 11.91: 4 Bond angle restraints: 27824 Sorted by residual: angle pdb=" C ARG I 430 " pdb=" N LYS I 431 " pdb=" CA LYS I 431 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta sigma weight residual 121.54 133.41 -11.87 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.67 106.00 5.67 9.50e-01 1.11e+00 3.56e+01 ... (remaining 27819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.51: 12055 20.51 - 41.03: 576 41.03 - 61.54: 102 61.54 - 82.05: 63 82.05 - 102.56: 24 Dihedral angle restraints: 12820 sinusoidal: 5708 harmonic: 7112 Sorted by residual: dihedral pdb=" CA ARG G 430 " pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta harmonic sigma weight residual -180.00 -143.33 -36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA ARG H 430 " pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta harmonic sigma weight residual -180.00 -143.45 -36.55 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ARG J 430 " pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta harmonic sigma weight residual -180.00 -143.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 12817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1388 0.056 - 0.113: 1105 0.113 - 0.169: 483 0.169 - 0.225: 185 0.225 - 0.282: 35 Chirality restraints: 3196 Sorted by residual: chirality pdb=" C1 MAN Q 4 " pdb=" O3 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.93e+01 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.67e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.11e+01 ... (remaining 3193 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.088 2.00e-02 2.50e+03 7.60e-02 7.21e+01 pdb=" C7 NAG Q 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.107 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.087 2.00e-02 2.50e+03 7.54e-02 7.11e+01 pdb=" C7 NAG F 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.087 2.00e-02 2.50e+03 7.48e-02 7.00e+01 pdb=" C7 NAG W 1 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.076 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2596 2.79 - 3.31: 19147 3.31 - 3.84: 35950 3.84 - 4.37: 46110 4.37 - 4.90: 73522 Nonbonded interactions: 177325 Sorted by model distance: nonbonded pdb=" O ASP G 293 " pdb="CA CA G1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP I 293 " pdb="CA CA I1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP H 293 " pdb="CA CA H1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP J 293 " pdb="CA CA J1103 " model vdw 2.265 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J1103 " model vdw 2.323 2.510 ... (remaining 177320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } ncs_group { reference = (chain 'G' and resid 82 through 1103) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.720 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 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 : 0.014 0.120 20592 Z= 0.989 Angle : 1.638 11.913 28080 Z= 1.045 Chirality : 0.092 0.282 3196 Planarity : 0.010 0.076 3500 Dihedral : 14.337 102.563 8160 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2476 helix: 0.14 (0.94), residues: 24 sheet: 0.03 (0.16), residues: 1012 loop : -0.88 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG G 156 TYR 0.060 0.013 TYR H 281 PHE 0.066 0.012 PHE G 205 TRP 0.094 0.016 TRP H 458 HIS 0.024 0.006 HIS H 168 Details of bonding type rmsd covalent geometry : bond 0.01388 (20492) covalent geometry : angle 1.61122 (27824) SS BOND : bond 0.06185 ( 44) SS BOND : angle 2.27667 ( 88) hydrogen bonds : bond 0.13550 ( 656) hydrogen bonds : angle 8.33451 ( 1728) link_ALPHA1-2 : bond 0.00384 ( 4) link_ALPHA1-2 : angle 5.62704 ( 12) link_ALPHA1-3 : bond 0.01399 ( 8) link_ALPHA1-3 : angle 3.16599 ( 24) link_ALPHA1-6 : bond 0.00930 ( 8) link_ALPHA1-6 : angle 2.39121 ( 24) link_BETA1-4 : bond 0.01402 ( 16) link_BETA1-4 : angle 4.05015 ( 48) link_NAG-ASN : bond 0.00720 ( 20) link_NAG-ASN : angle 4.25351 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.564 Fit side-chains REVERT: G 400 ARG cc_start: 0.8987 (ptm-80) cc_final: 0.8568 (ptm160) REVERT: G 467 MET cc_start: 0.9081 (ptm) cc_final: 0.8878 (ptm) REVERT: A 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8503 (mt-10) REVERT: A 62 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8282 (tp-100) REVERT: L 61 ARG cc_start: 0.9078 (ptt-90) cc_final: 0.8828 (ptt-90) REVERT: L 82 ASP cc_start: 0.9266 (m-30) cc_final: 0.9047 (m-30) REVERT: H 400 ARG cc_start: 0.8991 (ptm-80) cc_final: 0.8573 (ptm160) REVERT: B 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8498 (mt-10) REVERT: B 62 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8268 (tp-100) REVERT: M 61 ARG cc_start: 0.9084 (ptt-90) cc_final: 0.8832 (ptt-90) REVERT: M 82 ASP cc_start: 0.9269 (m-30) cc_final: 0.9049 (m-30) REVERT: I 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8558 (ptm160) REVERT: C 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8497 (mt-10) REVERT: C 62 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8283 (tp-100) REVERT: N 61 ARG cc_start: 0.9081 (ptt-90) cc_final: 0.8831 (ptt-90) REVERT: N 82 ASP cc_start: 0.9267 (m-30) cc_final: 0.9046 (m-30) REVERT: J 247 THR cc_start: 0.7304 (m) cc_final: 0.6837 (p) REVERT: J 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8559 (ptm160) REVERT: D 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8501 (mt-10) REVERT: D 62 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8331 (tp-100) REVERT: O 61 ARG cc_start: 0.9085 (ptt-90) cc_final: 0.8826 (ptt-90) REVERT: O 82 ASP cc_start: 0.9270 (m-30) cc_final: 0.9045 (m-30) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.6888 time to fit residues: 253.9875 Evaluate side-chains 277 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS A 65 GLN L 6 GLN H 347 HIS B 65 GLN M 6 GLN I 347 HIS C 65 GLN N 6 GLN J 347 HIS O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.069783 restraints weight = 27934.986| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.18 r_work: 0.2703 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20592 Z= 0.166 Angle : 0.673 7.230 28080 Z= 0.359 Chirality : 0.047 0.159 3196 Planarity : 0.004 0.032 3500 Dihedral : 9.251 78.297 3848 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.25 % Rotamer: Outliers : 1.46 % Allowed : 8.49 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2476 helix: -0.35 (0.87), residues: 24 sheet: 0.26 (0.15), residues: 1060 loop : -0.12 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 27 TYR 0.014 0.002 TYR J 121 PHE 0.013 0.002 PHE J 410 TRP 0.020 0.002 TRP H 115 HIS 0.005 0.001 HIS J 347 Details of bonding type rmsd covalent geometry : bond 0.00364 (20492) covalent geometry : angle 0.64805 (27824) SS BOND : bond 0.00340 ( 44) SS BOND : angle 0.74211 ( 88) hydrogen bonds : bond 0.04823 ( 656) hydrogen bonds : angle 6.82130 ( 1728) link_ALPHA1-2 : bond 0.00385 ( 4) link_ALPHA1-2 : angle 2.35952 ( 12) link_ALPHA1-3 : bond 0.00952 ( 8) link_ALPHA1-3 : angle 2.13645 ( 24) link_ALPHA1-6 : bond 0.00616 ( 8) link_ALPHA1-6 : angle 1.38185 ( 24) link_BETA1-4 : bond 0.00506 ( 16) link_BETA1-4 : angle 2.01723 ( 48) link_NAG-ASN : bond 0.00145 ( 20) link_NAG-ASN : angle 3.04343 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 0.823 Fit side-chains REVERT: G 400 ARG cc_start: 0.8421 (ptm-80) cc_final: 0.7845 (ptm160) REVERT: A 62 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7504 (tp-100) REVERT: L 61 ARG cc_start: 0.8863 (ptt-90) cc_final: 0.8489 (ptt-90) REVERT: L 82 ASP cc_start: 0.9107 (m-30) cc_final: 0.8792 (m-30) REVERT: L 101 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8327 (mm110) REVERT: H 400 ARG cc_start: 0.8430 (ptm-80) cc_final: 0.7844 (ptm160) REVERT: B 62 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7533 (tp-100) REVERT: M 61 ARG cc_start: 0.8871 (ptt-90) cc_final: 0.8494 (ptt-90) REVERT: M 82 ASP cc_start: 0.9102 (m-30) cc_final: 0.8784 (m-30) REVERT: M 101 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8335 (mm110) REVERT: I 400 ARG cc_start: 0.8402 (ptm-80) cc_final: 0.7856 (ptm160) REVERT: C 62 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7509 (tp-100) REVERT: N 61 ARG cc_start: 0.8877 (ptt-90) cc_final: 0.8506 (ptt-90) REVERT: N 82 ASP cc_start: 0.9105 (m-30) cc_final: 0.8794 (m-30) REVERT: N 101 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8324 (mm110) REVERT: J 400 ARG cc_start: 0.8391 (ptm-80) cc_final: 0.7851 (ptm160) REVERT: D 62 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7721 (mm-40) REVERT: O 61 ARG cc_start: 0.8879 (ptt-90) cc_final: 0.8508 (ptt-90) REVERT: O 82 ASP cc_start: 0.9113 (m-30) cc_final: 0.8801 (m-30) REVERT: O 101 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8333 (mm110) outliers start: 31 outliers final: 4 residues processed: 285 average time/residue: 0.6856 time to fit residues: 218.3268 Evaluate side-chains 260 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 256 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 190 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 215 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 65 GLN L 6 GLN B 65 GLN M 6 GLN C 30 ASN C 65 GLN N 6 GLN J 141 ASN D 30 ASN O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.069663 restraints weight = 28176.733| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.18 r_work: 0.2710 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20592 Z= 0.160 Angle : 0.617 6.276 28080 Z= 0.327 Chirality : 0.046 0.171 3196 Planarity : 0.003 0.039 3500 Dihedral : 8.268 67.910 3848 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.63 % Favored : 97.05 % Rotamer: Outliers : 2.17 % Allowed : 9.67 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.17), residues: 2476 helix: 0.35 (0.94), residues: 24 sheet: 0.40 (0.15), residues: 1060 loop : -0.07 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 85 TYR 0.014 0.002 TYR H 121 PHE 0.012 0.002 PHE I 354 TRP 0.018 0.002 TRP H 178 HIS 0.003 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00353 (20492) covalent geometry : angle 0.59591 (27824) SS BOND : bond 0.00263 ( 44) SS BOND : angle 0.57665 ( 88) hydrogen bonds : bond 0.04335 ( 656) hydrogen bonds : angle 6.27390 ( 1728) link_ALPHA1-2 : bond 0.00287 ( 4) link_ALPHA1-2 : angle 2.48007 ( 12) link_ALPHA1-3 : bond 0.00785 ( 8) link_ALPHA1-3 : angle 1.96035 ( 24) link_ALPHA1-6 : bond 0.00535 ( 8) link_ALPHA1-6 : angle 1.36159 ( 24) link_BETA1-4 : bond 0.00493 ( 16) link_BETA1-4 : angle 1.76217 ( 48) link_NAG-ASN : bond 0.00124 ( 20) link_NAG-ASN : angle 2.63305 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.815 Fit side-chains REVERT: G 400 ARG cc_start: 0.8465 (ptm-80) cc_final: 0.7831 (ptm160) REVERT: A 62 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7487 (tp-100) REVERT: L 61 ARG cc_start: 0.8846 (ptt-90) cc_final: 0.8477 (ptt-90) REVERT: L 101 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8492 (mm110) REVERT: H 400 ARG cc_start: 0.8460 (ptm-80) cc_final: 0.7831 (ptm160) REVERT: B 62 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7489 (tp-100) REVERT: M 61 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8481 (ptt-90) REVERT: M 101 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8496 (mm110) REVERT: I 400 ARG cc_start: 0.8430 (ptm-80) cc_final: 0.7800 (ptm160) REVERT: C 62 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7516 (tp-100) REVERT: N 61 ARG cc_start: 0.8853 (ptt-90) cc_final: 0.8487 (ptt-90) REVERT: N 101 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8491 (mm110) REVERT: J 400 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.7799 (ptm160) REVERT: D 62 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7684 (tp-100) REVERT: O 61 ARG cc_start: 0.8840 (ptt-90) cc_final: 0.8483 (ptt-90) REVERT: O 101 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8475 (mm110) outliers start: 46 outliers final: 23 residues processed: 291 average time/residue: 0.6377 time to fit residues: 208.6632 Evaluate side-chains 275 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 21 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 30 ASN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.067086 restraints weight = 28276.736| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.17 r_work: 0.2660 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20592 Z= 0.272 Angle : 0.675 7.014 28080 Z= 0.355 Chirality : 0.049 0.180 3196 Planarity : 0.004 0.044 3500 Dihedral : 8.592 71.122 3848 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.07 % Favored : 96.61 % Rotamer: Outliers : 1.89 % Allowed : 9.91 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2476 helix: 0.38 (0.94), residues: 24 sheet: 0.24 (0.15), residues: 1016 loop : -0.14 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 85 TYR 0.015 0.002 TYR H 121 PHE 0.014 0.002 PHE H 410 TRP 0.017 0.002 TRP J 115 HIS 0.004 0.001 HIS H 168 Details of bonding type rmsd covalent geometry : bond 0.00618 (20492) covalent geometry : angle 0.65006 (27824) SS BOND : bond 0.00374 ( 44) SS BOND : angle 1.03353 ( 88) hydrogen bonds : bond 0.04855 ( 656) hydrogen bonds : angle 6.40009 ( 1728) link_ALPHA1-2 : bond 0.00095 ( 4) link_ALPHA1-2 : angle 2.81884 ( 12) link_ALPHA1-3 : bond 0.00434 ( 8) link_ALPHA1-3 : angle 2.31481 ( 24) link_ALPHA1-6 : bond 0.00329 ( 8) link_ALPHA1-6 : angle 1.51950 ( 24) link_BETA1-4 : bond 0.00374 ( 16) link_BETA1-4 : angle 1.87992 ( 48) link_NAG-ASN : bond 0.00308 ( 20) link_NAG-ASN : angle 2.84622 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.578 Fit side-chains REVERT: G 400 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.7877 (ptm160) REVERT: A 62 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7610 (tp-100) REVERT: L 61 ARG cc_start: 0.8838 (ptt-90) cc_final: 0.8373 (ptt-90) REVERT: H 400 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.7890 (ptm160) REVERT: B 62 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7623 (tp-100) REVERT: M 61 ARG cc_start: 0.8837 (ptt-90) cc_final: 0.8375 (ptt-90) REVERT: I 400 ARG cc_start: 0.8548 (ptm-80) cc_final: 0.7863 (ptm160) REVERT: C 62 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7613 (tp-100) REVERT: N 61 ARG cc_start: 0.8838 (ptt-90) cc_final: 0.8376 (ptt-90) REVERT: J 400 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.7857 (ptm160) REVERT: D 62 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7713 (tp-100) REVERT: O 61 ARG cc_start: 0.8847 (ptt-90) cc_final: 0.8378 (ptt-90) outliers start: 40 outliers final: 33 residues processed: 269 average time/residue: 0.6365 time to fit residues: 192.3160 Evaluate side-chains 274 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 0.9990 chunk 199 optimal weight: 0.3980 chunk 98 optimal weight: 7.9990 chunk 175 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 189 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 235 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 30 ASN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.071098 restraints weight = 27929.585| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.18 r_work: 0.2742 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20592 Z= 0.111 Angle : 0.574 8.119 28080 Z= 0.301 Chirality : 0.045 0.179 3196 Planarity : 0.003 0.041 3500 Dihedral : 7.518 59.482 3848 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.50 % Favored : 97.25 % Rotamer: Outliers : 1.08 % Allowed : 10.85 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.16), residues: 2476 helix: -0.48 (0.84), residues: 28 sheet: 0.25 (0.15), residues: 1040 loop : -0.07 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 85 TYR 0.011 0.001 TYR H 121 PHE 0.013 0.002 PHE J 410 TRP 0.019 0.001 TRP I 178 HIS 0.002 0.001 HIS J 274 Details of bonding type rmsd covalent geometry : bond 0.00234 (20492) covalent geometry : angle 0.55631 (27824) SS BOND : bond 0.00179 ( 44) SS BOND : angle 0.59610 ( 88) hydrogen bonds : bond 0.03727 ( 656) hydrogen bonds : angle 5.93064 ( 1728) link_ALPHA1-2 : bond 0.00407 ( 4) link_ALPHA1-2 : angle 2.22444 ( 12) link_ALPHA1-3 : bond 0.00947 ( 8) link_ALPHA1-3 : angle 1.74838 ( 24) link_ALPHA1-6 : bond 0.00596 ( 8) link_ALPHA1-6 : angle 1.35496 ( 24) link_BETA1-4 : bond 0.00544 ( 16) link_BETA1-4 : angle 1.45421 ( 48) link_NAG-ASN : bond 0.00064 ( 20) link_NAG-ASN : angle 2.29300 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 0.829 Fit side-chains REVERT: G 400 ARG cc_start: 0.8465 (ptm-80) cc_final: 0.7774 (ptm160) REVERT: G 435 GLU cc_start: 0.8808 (mp0) cc_final: 0.8606 (mp0) REVERT: A 62 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7481 (tp-100) REVERT: L 61 ARG cc_start: 0.8843 (ptt-90) cc_final: 0.8416 (ptt-90) REVERT: H 400 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.7790 (ptm160) REVERT: H 435 GLU cc_start: 0.8810 (mp0) cc_final: 0.8608 (mp0) REVERT: B 62 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7495 (tp-100) REVERT: M 61 ARG cc_start: 0.8834 (ptt-90) cc_final: 0.8410 (ptt-90) REVERT: I 400 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.7774 (ptm160) REVERT: I 435 GLU cc_start: 0.8817 (mp0) cc_final: 0.8616 (mp0) REVERT: C 62 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7474 (tp-100) REVERT: N 61 ARG cc_start: 0.8840 (ptt-90) cc_final: 0.8418 (ptt-90) REVERT: J 400 ARG cc_start: 0.8437 (ptm-80) cc_final: 0.7765 (ptm160) REVERT: D 62 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7636 (tp-100) REVERT: O 61 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8417 (ptt-90) outliers start: 23 outliers final: 12 residues processed: 263 average time/residue: 0.7072 time to fit residues: 208.1216 Evaluate side-chains 267 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 255 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 230 optimal weight: 0.0870 chunk 19 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 174 optimal weight: 0.0670 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.070915 restraints weight = 27956.911| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.18 r_work: 0.2739 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20592 Z= 0.127 Angle : 0.574 8.105 28080 Z= 0.299 Chirality : 0.045 0.201 3196 Planarity : 0.003 0.042 3500 Dihedral : 7.195 55.632 3848 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 1.32 % Allowed : 11.46 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.16), residues: 2476 helix: -1.72 (0.61), residues: 52 sheet: 0.32 (0.15), residues: 1032 loop : -0.04 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 85 TYR 0.012 0.001 TYR H 121 PHE 0.013 0.002 PHE H 410 TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00274 (20492) covalent geometry : angle 0.55615 (27824) SS BOND : bond 0.00207 ( 44) SS BOND : angle 0.51789 ( 88) hydrogen bonds : bond 0.03809 ( 656) hydrogen bonds : angle 5.85739 ( 1728) link_ALPHA1-2 : bond 0.00269 ( 4) link_ALPHA1-2 : angle 2.28092 ( 12) link_ALPHA1-3 : bond 0.00794 ( 8) link_ALPHA1-3 : angle 1.86742 ( 24) link_ALPHA1-6 : bond 0.00554 ( 8) link_ALPHA1-6 : angle 1.44117 ( 24) link_BETA1-4 : bond 0.00466 ( 16) link_BETA1-4 : angle 1.49601 ( 48) link_NAG-ASN : bond 0.00083 ( 20) link_NAG-ASN : angle 2.32046 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.832 Fit side-chains REVERT: G 400 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.7772 (ptm160) REVERT: G 435 GLU cc_start: 0.8765 (mp0) cc_final: 0.8532 (mp0) REVERT: A 62 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7475 (tp-100) REVERT: A 65 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: A 89 GLU cc_start: 0.8987 (pm20) cc_final: 0.8753 (pm20) REVERT: L 61 ARG cc_start: 0.8778 (ptt-90) cc_final: 0.8452 (ptt-90) REVERT: H 400 ARG cc_start: 0.8473 (ptm-80) cc_final: 0.7782 (ptm160) REVERT: H 435 GLU cc_start: 0.8770 (mp0) cc_final: 0.8539 (mp0) REVERT: B 62 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7479 (tp-100) REVERT: M 61 ARG cc_start: 0.8774 (ptt-90) cc_final: 0.8453 (ptt-90) REVERT: I 400 ARG cc_start: 0.8454 (ptm-80) cc_final: 0.7770 (ptm160) REVERT: I 435 GLU cc_start: 0.8769 (mp0) cc_final: 0.8538 (mp0) REVERT: C 62 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7445 (tp-100) REVERT: C 65 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: C 89 GLU cc_start: 0.8995 (pm20) cc_final: 0.8763 (pm20) REVERT: N 61 ARG cc_start: 0.8779 (ptt-90) cc_final: 0.8458 (ptt-90) REVERT: J 400 ARG cc_start: 0.8450 (ptm-80) cc_final: 0.7767 (ptm160) REVERT: D 62 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7657 (tp-100) REVERT: D 89 GLU cc_start: 0.8999 (pm20) cc_final: 0.8765 (pm20) REVERT: O 61 ARG cc_start: 0.8789 (ptt-90) cc_final: 0.8460 (ptt-90) outliers start: 28 outliers final: 17 residues processed: 276 average time/residue: 0.6905 time to fit residues: 213.9445 Evaluate side-chains 272 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 13 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN N 6 GLN N 70 GLN J 220 ASN O 6 GLN O 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.068862 restraints weight = 28134.997| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.19 r_work: 0.2696 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20592 Z= 0.201 Angle : 0.621 7.924 28080 Z= 0.324 Chirality : 0.047 0.206 3196 Planarity : 0.004 0.043 3500 Dihedral : 7.522 58.897 3848 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 0.85 % Allowed : 12.78 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 2476 helix: -1.76 (0.62), residues: 52 sheet: 0.23 (0.15), residues: 1060 loop : 0.02 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 19 TYR 0.013 0.002 TYR H 121 PHE 0.013 0.002 PHE G 410 TRP 0.013 0.002 TRP J 178 HIS 0.003 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00453 (20492) covalent geometry : angle 0.60050 (27824) SS BOND : bond 0.00327 ( 44) SS BOND : angle 0.99729 ( 88) hydrogen bonds : bond 0.04262 ( 656) hydrogen bonds : angle 6.03452 ( 1728) link_ALPHA1-2 : bond 0.00110 ( 4) link_ALPHA1-2 : angle 2.44348 ( 12) link_ALPHA1-3 : bond 0.00610 ( 8) link_ALPHA1-3 : angle 2.08093 ( 24) link_ALPHA1-6 : bond 0.00418 ( 8) link_ALPHA1-6 : angle 1.48338 ( 24) link_BETA1-4 : bond 0.00398 ( 16) link_BETA1-4 : angle 1.59283 ( 48) link_NAG-ASN : bond 0.00191 ( 20) link_NAG-ASN : angle 2.45895 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 0.821 Fit side-chains REVERT: G 400 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.7790 (ptm160) REVERT: G 435 GLU cc_start: 0.8788 (mp0) cc_final: 0.8565 (mp0) REVERT: A 19 ARG cc_start: 0.9092 (ttt-90) cc_final: 0.8789 (ttt-90) REVERT: A 62 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7560 (tp-100) REVERT: A 82 GLU cc_start: 0.8178 (tt0) cc_final: 0.7581 (mm-30) REVERT: A 89 GLU cc_start: 0.8973 (pm20) cc_final: 0.8732 (pm20) REVERT: L 61 ARG cc_start: 0.8778 (ptt-90) cc_final: 0.8415 (ptt-90) REVERT: H 400 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.7803 (ptm160) REVERT: H 435 GLU cc_start: 0.8793 (mp0) cc_final: 0.8573 (mp0) REVERT: B 62 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7545 (tp-100) REVERT: B 65 GLN cc_start: 0.7629 (tt0) cc_final: 0.7380 (tt0) REVERT: B 89 GLU cc_start: 0.8977 (pm20) cc_final: 0.8736 (pm20) REVERT: M 61 ARG cc_start: 0.8776 (ptt-90) cc_final: 0.8413 (ptt-90) REVERT: I 400 ARG cc_start: 0.8512 (ptm-80) cc_final: 0.7784 (ptm160) REVERT: I 435 GLU cc_start: 0.8795 (mp0) cc_final: 0.8575 (mp0) REVERT: C 19 ARG cc_start: 0.9098 (ttt-90) cc_final: 0.8765 (ttt-90) REVERT: C 62 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7559 (tp-100) REVERT: C 82 GLU cc_start: 0.8194 (tt0) cc_final: 0.7574 (mm-30) REVERT: C 89 GLU cc_start: 0.8985 (pm20) cc_final: 0.8752 (pm20) REVERT: N 61 ARG cc_start: 0.8783 (ptt-90) cc_final: 0.8425 (ptt-90) REVERT: J 400 ARG cc_start: 0.8514 (ptm-80) cc_final: 0.7786 (ptm160) REVERT: D 19 ARG cc_start: 0.9101 (ttt-90) cc_final: 0.8768 (ttt-90) REVERT: D 62 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7665 (tp-100) REVERT: D 82 GLU cc_start: 0.8166 (tt0) cc_final: 0.7559 (mm-30) REVERT: D 89 GLU cc_start: 0.8992 (pm20) cc_final: 0.8759 (pm20) REVERT: O 61 ARG cc_start: 0.8792 (ptt-90) cc_final: 0.8426 (ptt-90) outliers start: 18 outliers final: 17 residues processed: 264 average time/residue: 0.7087 time to fit residues: 209.5093 Evaluate side-chains 268 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 85 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 220 ASN A 65 GLN L 6 GLN L 70 GLN H 220 ASN M 6 GLN M 70 GLN I 220 ASN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.069572 restraints weight = 28122.565| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.17 r_work: 0.2709 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20592 Z= 0.166 Angle : 0.602 8.391 28080 Z= 0.314 Chirality : 0.046 0.198 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.431 58.073 3848 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.97 % Rotamer: Outliers : 0.94 % Allowed : 12.92 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2476 helix: -1.79 (0.61), residues: 52 sheet: 0.26 (0.16), residues: 960 loop : -0.02 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.012 0.001 TYR H 121 PHE 0.013 0.002 PHE H 410 TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS J 144 Details of bonding type rmsd covalent geometry : bond 0.00367 (20492) covalent geometry : angle 0.58293 (27824) SS BOND : bond 0.00247 ( 44) SS BOND : angle 0.78710 ( 88) hydrogen bonds : bond 0.04083 ( 656) hydrogen bonds : angle 5.98402 ( 1728) link_ALPHA1-2 : bond 0.00150 ( 4) link_ALPHA1-2 : angle 2.33608 ( 12) link_ALPHA1-3 : bond 0.00702 ( 8) link_ALPHA1-3 : angle 1.98917 ( 24) link_ALPHA1-6 : bond 0.00453 ( 8) link_ALPHA1-6 : angle 1.45865 ( 24) link_BETA1-4 : bond 0.00443 ( 16) link_BETA1-4 : angle 1.52258 ( 48) link_NAG-ASN : bond 0.00145 ( 20) link_NAG-ASN : angle 2.39069 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.834 Fit side-chains REVERT: G 400 ARG cc_start: 0.8521 (ptm-80) cc_final: 0.7784 (ptm160) REVERT: A 19 ARG cc_start: 0.9111 (ttt-90) cc_final: 0.8796 (ttt-90) REVERT: A 62 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7562 (tp-100) REVERT: A 65 GLN cc_start: 0.7686 (tt0) cc_final: 0.7440 (tt0) REVERT: A 82 GLU cc_start: 0.8215 (tt0) cc_final: 0.7643 (mm-30) REVERT: L 61 ARG cc_start: 0.8778 (ptt-90) cc_final: 0.8394 (ptt-90) REVERT: H 400 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.7791 (ptm160) REVERT: B 62 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7563 (tp-100) REVERT: B 65 GLN cc_start: 0.7680 (tt0) cc_final: 0.7455 (tt0) REVERT: B 82 GLU cc_start: 0.8226 (tt0) cc_final: 0.7720 (mm-30) REVERT: B 89 GLU cc_start: 0.8994 (pm20) cc_final: 0.8750 (pm20) REVERT: M 61 ARG cc_start: 0.8775 (ptt-90) cc_final: 0.8393 (ptt-90) REVERT: I 400 ARG cc_start: 0.8515 (ptm-80) cc_final: 0.7780 (ptm160) REVERT: C 19 ARG cc_start: 0.9130 (ttt-90) cc_final: 0.8805 (ttt-90) REVERT: C 62 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7555 (tp-100) REVERT: C 65 GLN cc_start: 0.7682 (tt0) cc_final: 0.7434 (tt0) REVERT: C 82 GLU cc_start: 0.8200 (tt0) cc_final: 0.7618 (mm-30) REVERT: N 61 ARG cc_start: 0.8782 (ptt-90) cc_final: 0.8402 (ptt-90) REVERT: J 400 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.7789 (ptm160) REVERT: D 19 ARG cc_start: 0.9135 (ttt-90) cc_final: 0.8819 (ttt-90) REVERT: D 62 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7667 (tp-100) REVERT: D 82 GLU cc_start: 0.8187 (tt0) cc_final: 0.7615 (mm-30) REVERT: O 61 ARG cc_start: 0.8790 (ptt-90) cc_final: 0.8406 (ptt-90) outliers start: 20 outliers final: 18 residues processed: 263 average time/residue: 0.7087 time to fit residues: 208.8036 Evaluate side-chains 268 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 232 optimal weight: 0.0770 chunk 130 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 70 GLN M 6 GLN M 70 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.068848 restraints weight = 28083.606| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.18 r_work: 0.2694 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20592 Z= 0.191 Angle : 0.623 8.298 28080 Z= 0.324 Chirality : 0.046 0.199 3196 Planarity : 0.004 0.043 3500 Dihedral : 7.573 59.346 3848 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.94 % Allowed : 13.02 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2476 helix: -1.82 (0.61), residues: 52 sheet: 0.27 (0.15), residues: 1056 loop : -0.07 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.013 0.001 TYR I 121 PHE 0.014 0.002 PHE G 410 TRP 0.014 0.002 TRP H 178 HIS 0.002 0.001 HIS I 184 Details of bonding type rmsd covalent geometry : bond 0.00427 (20492) covalent geometry : angle 0.60325 (27824) SS BOND : bond 0.00266 ( 44) SS BOND : angle 0.80096 ( 88) hydrogen bonds : bond 0.04248 ( 656) hydrogen bonds : angle 6.05188 ( 1728) link_ALPHA1-2 : bond 0.00049 ( 4) link_ALPHA1-2 : angle 2.37711 ( 12) link_ALPHA1-3 : bond 0.00600 ( 8) link_ALPHA1-3 : angle 2.07585 ( 24) link_ALPHA1-6 : bond 0.00398 ( 8) link_ALPHA1-6 : angle 1.48831 ( 24) link_BETA1-4 : bond 0.00410 ( 16) link_BETA1-4 : angle 1.57419 ( 48) link_NAG-ASN : bond 0.00182 ( 20) link_NAG-ASN : angle 2.45582 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.793 Fit side-chains REVERT: G 400 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.7791 (ptm160) REVERT: A 19 ARG cc_start: 0.9107 (ttt-90) cc_final: 0.8829 (ttt-90) REVERT: A 62 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7619 (tp-100) REVERT: A 65 GLN cc_start: 0.7711 (tt0) cc_final: 0.7475 (tt0) REVERT: A 82 GLU cc_start: 0.8198 (tt0) cc_final: 0.7619 (mm-30) REVERT: L 61 ARG cc_start: 0.8778 (ptt-90) cc_final: 0.8379 (ptt-90) REVERT: H 400 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.7790 (ptm160) REVERT: B 62 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7590 (tp-100) REVERT: B 65 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: B 82 GLU cc_start: 0.8246 (tt0) cc_final: 0.7711 (mm-30) REVERT: M 61 ARG cc_start: 0.8775 (ptt-90) cc_final: 0.8378 (ptt-90) REVERT: I 400 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.7788 (ptm160) REVERT: C 19 ARG cc_start: 0.9127 (ttt-90) cc_final: 0.8791 (ttt-90) REVERT: C 62 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7613 (tp-100) REVERT: C 65 GLN cc_start: 0.7699 (tt0) cc_final: 0.7460 (tt0) REVERT: C 82 GLU cc_start: 0.8194 (tt0) cc_final: 0.7597 (mm-30) REVERT: N 61 ARG cc_start: 0.8787 (ptt-90) cc_final: 0.8394 (ptt-90) REVERT: J 400 ARG cc_start: 0.8541 (ptm-80) cc_final: 0.7791 (ptm160) REVERT: D 19 ARG cc_start: 0.9129 (ttt-90) cc_final: 0.8796 (ttt-90) REVERT: D 62 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7670 (tp-100) REVERT: D 82 GLU cc_start: 0.8187 (tt0) cc_final: 0.7594 (mm-30) REVERT: O 61 ARG cc_start: 0.8780 (ptt-90) cc_final: 0.8382 (ptt-90) outliers start: 20 outliers final: 19 residues processed: 259 average time/residue: 0.6846 time to fit residues: 198.9275 Evaluate side-chains 269 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 87 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 70 GLN M 6 GLN M 70 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.070055 restraints weight = 28101.083| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.18 r_work: 0.2722 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20592 Z= 0.146 Angle : 0.596 8.401 28080 Z= 0.310 Chirality : 0.045 0.197 3196 Planarity : 0.003 0.042 3500 Dihedral : 7.283 56.102 3848 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 1.04 % Allowed : 13.11 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2476 helix: -1.80 (0.60), residues: 52 sheet: 0.24 (0.15), residues: 1068 loop : -0.03 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.012 0.001 TYR H 121 PHE 0.014 0.002 PHE M 83 TRP 0.016 0.001 TRP I 178 HIS 0.002 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00323 (20492) covalent geometry : angle 0.57881 (27824) SS BOND : bond 0.00215 ( 44) SS BOND : angle 0.69494 ( 88) hydrogen bonds : bond 0.03933 ( 656) hydrogen bonds : angle 5.91636 ( 1728) link_ALPHA1-2 : bond 0.00162 ( 4) link_ALPHA1-2 : angle 2.21397 ( 12) link_ALPHA1-3 : bond 0.00742 ( 8) link_ALPHA1-3 : angle 1.89637 ( 24) link_ALPHA1-6 : bond 0.00481 ( 8) link_ALPHA1-6 : angle 1.44524 ( 24) link_BETA1-4 : bond 0.00448 ( 16) link_BETA1-4 : angle 1.46119 ( 48) link_NAG-ASN : bond 0.00113 ( 20) link_NAG-ASN : angle 2.29516 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.758 Fit side-chains REVERT: G 400 ARG cc_start: 0.8525 (ptm-80) cc_final: 0.7775 (ptm160) REVERT: A 19 ARG cc_start: 0.9107 (ttt-90) cc_final: 0.8839 (ttt-90) REVERT: A 62 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7556 (tp-100) REVERT: A 65 GLN cc_start: 0.7675 (tt0) cc_final: 0.7441 (tt0) REVERT: A 82 GLU cc_start: 0.8230 (tt0) cc_final: 0.7637 (mm-30) REVERT: L 61 ARG cc_start: 0.8780 (ptt-90) cc_final: 0.8408 (ptt-90) REVERT: H 400 ARG cc_start: 0.8525 (ptm-80) cc_final: 0.7787 (ptm160) REVERT: B 19 ARG cc_start: 0.9098 (ttt-90) cc_final: 0.8890 (ttt90) REVERT: B 62 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7610 (tp-100) REVERT: B 65 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: B 82 GLU cc_start: 0.8252 (tt0) cc_final: 0.7930 (tp30) REVERT: M 61 ARG cc_start: 0.8776 (ptt-90) cc_final: 0.8406 (ptt-90) REVERT: I 400 ARG cc_start: 0.8510 (ptm-80) cc_final: 0.7767 (ptm160) REVERT: C 19 ARG cc_start: 0.9111 (ttt-90) cc_final: 0.8784 (ttt-90) REVERT: C 62 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7556 (tp-100) REVERT: C 65 GLN cc_start: 0.7711 (tt0) cc_final: 0.7477 (tt0) REVERT: C 82 GLU cc_start: 0.8204 (tt0) cc_final: 0.7617 (mm-30) REVERT: N 61 ARG cc_start: 0.8779 (ptt-90) cc_final: 0.8412 (ptt-90) REVERT: J 400 ARG cc_start: 0.8516 (ptm-80) cc_final: 0.7770 (ptm160) REVERT: D 19 ARG cc_start: 0.9113 (ttt-90) cc_final: 0.8793 (ttt-90) REVERT: D 62 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7729 (tp-100) REVERT: D 82 GLU cc_start: 0.8205 (tt0) cc_final: 0.7601 (mm-30) REVERT: O 61 ARG cc_start: 0.8792 (ptt-90) cc_final: 0.8423 (ptt-90) outliers start: 22 outliers final: 21 residues processed: 265 average time/residue: 0.6943 time to fit residues: 205.9711 Evaluate side-chains 275 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 18 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN ** O 70 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 = 0.3310 r_free = 0.3310 target = 0.097444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.069228 restraints weight = 28150.531| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.18 r_work: 0.2705 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20592 Z= 0.179 Angle : 0.616 8.317 28080 Z= 0.320 Chirality : 0.046 0.200 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.391 57.211 3848 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 1.04 % Allowed : 13.58 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2476 helix: -1.80 (0.60), residues: 52 sheet: 0.21 (0.15), residues: 1068 loop : -0.05 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.013 0.001 TYR H 121 PHE 0.013 0.002 PHE H 410 TRP 0.014 0.002 TRP I 178 HIS 0.002 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00401 (20492) covalent geometry : angle 0.59743 (27824) SS BOND : bond 0.00259 ( 44) SS BOND : angle 0.79658 ( 88) hydrogen bonds : bond 0.04139 ( 656) hydrogen bonds : angle 6.00280 ( 1728) link_ALPHA1-2 : bond 0.00056 ( 4) link_ALPHA1-2 : angle 2.26255 ( 12) link_ALPHA1-3 : bond 0.00647 ( 8) link_ALPHA1-3 : angle 2.03687 ( 24) link_ALPHA1-6 : bond 0.00410 ( 8) link_ALPHA1-6 : angle 1.48415 ( 24) link_BETA1-4 : bond 0.00414 ( 16) link_BETA1-4 : angle 1.52817 ( 48) link_NAG-ASN : bond 0.00161 ( 20) link_NAG-ASN : angle 2.38874 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8212.33 seconds wall clock time: 140 minutes 48.70 seconds (8448.70 seconds total)