Starting phenix.real_space_refine on Tue Jun 17 18:21:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3v_29710/06_2025/8g3v_29710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3v_29710/06_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_29710/06_2025/8g3v_29710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3v_29710/06_2025/8g3v_29710.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3v_29710/06_2025/8g3v_29710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3v_29710/06_2025/8g3v_29710.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.23, per 1000 atoms: 0.61 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: 5.03 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.73 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: 7.00 Time building geometry restraints manager: 5.93 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 469 or resid 1101 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 45.590 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (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 TRP 0.094 0.016 TRP H 458 HIS 0.024 0.006 HIS H 168 PHE 0.066 0.012 PHE G 205 TYR 0.060 0.013 TYR H 281 ARG 0.020 0.003 ARG G 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 20) link_NAG-ASN : angle 4.25351 ( 60) 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_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) hydrogen bonds : bond 0.13550 ( 656) hydrogen bonds : angle 8.33451 ( 1728) SS BOND : bond 0.06185 ( 44) SS BOND : angle 2.27667 ( 88) covalent geometry : bond 0.01388 (20492) covalent geometry : angle 1.61122 (27824) *********************** 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 : 2.669 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: 1.8648 time to fit residues: 690.9714 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 : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3313 r_free = 0.3313 target = 0.098315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.069738 restraints weight = 27830.696| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.18 r_work: 0.2701 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20592 Z= 0.166 Angle : 0.680 7.178 28080 Z= 0.364 Chirality : 0.048 0.155 3196 Planarity : 0.004 0.033 3500 Dihedral : 9.310 78.798 3848 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.25 % Rotamer: Outliers : 1.27 % Allowed : 8.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2476 helix: -0.43 (0.84), residues: 24 sheet: 0.24 (0.15), residues: 1080 loop : -0.10 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 178 HIS 0.005 0.001 HIS J 347 PHE 0.013 0.002 PHE J 410 TYR 0.014 0.002 TYR J 121 ARG 0.003 0.001 ARG I 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 20) link_NAG-ASN : angle 3.04093 ( 60) link_ALPHA1-6 : bond 0.00674 ( 8) link_ALPHA1-6 : angle 1.40869 ( 24) link_BETA1-4 : bond 0.00565 ( 16) link_BETA1-4 : angle 1.98224 ( 48) link_ALPHA1-2 : bond 0.00486 ( 4) link_ALPHA1-2 : angle 2.46145 ( 12) link_ALPHA1-3 : bond 0.00964 ( 8) link_ALPHA1-3 : angle 2.01438 ( 24) hydrogen bonds : bond 0.04907 ( 656) hydrogen bonds : angle 6.84166 ( 1728) SS BOND : bond 0.00319 ( 44) SS BOND : angle 0.74589 ( 88) covalent geometry : bond 0.00356 (20492) covalent geometry : angle 0.65575 (27824) *********************** 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 304 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 2.293 Fit side-chains REVERT: G 400 ARG cc_start: 0.8425 (ptm-80) cc_final: 0.7849 (ptm160) REVERT: A 62 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7509 (tp-100) REVERT: L 61 ARG cc_start: 0.8886 (ptt-90) cc_final: 0.8522 (ptt-90) REVERT: L 82 ASP cc_start: 0.9109 (m-30) cc_final: 0.8799 (m-30) REVERT: L 101 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8333 (mm110) REVERT: H 400 ARG cc_start: 0.8453 (ptm-80) cc_final: 0.7869 (ptm160) REVERT: B 62 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7539 (tp-100) REVERT: M 61 ARG cc_start: 0.8893 (ptt-90) cc_final: 0.8525 (ptt-90) REVERT: M 82 ASP cc_start: 0.9103 (m-30) cc_final: 0.8792 (m-30) REVERT: M 101 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8334 (mm110) REVERT: I 400 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.7862 (ptm160) REVERT: C 62 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7511 (tp-100) REVERT: N 61 ARG cc_start: 0.8899 (ptt-90) cc_final: 0.8537 (ptt-90) REVERT: N 82 ASP cc_start: 0.9108 (m-30) cc_final: 0.8802 (m-30) REVERT: N 101 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8329 (mm110) REVERT: J 400 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.7855 (ptm160) REVERT: D 62 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7737 (mm-40) REVERT: O 61 ARG cc_start: 0.8893 (ptt-90) cc_final: 0.8531 (ptt-90) REVERT: O 82 ASP cc_start: 0.9113 (m-30) cc_final: 0.8807 (m-30) REVERT: O 101 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8322 (mm110) outliers start: 27 outliers final: 8 residues processed: 285 average time/residue: 1.5258 time to fit residues: 487.7785 Evaluate side-chains 264 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 256 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 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 54 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 197 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.096538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.068158 restraints weight = 28074.064| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.16 r_work: 0.2678 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20592 Z= 0.219 Angle : 0.656 6.222 28080 Z= 0.348 Chirality : 0.048 0.171 3196 Planarity : 0.004 0.040 3500 Dihedral : 8.659 71.970 3848 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.07 % Favored : 96.61 % Rotamer: Outliers : 2.08 % Allowed : 9.62 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2476 helix: 0.24 (0.94), residues: 24 sheet: 0.40 (0.16), residues: 1012 loop : -0.13 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 115 HIS 0.004 0.001 HIS H 168 PHE 0.013 0.002 PHE H 410 TYR 0.015 0.002 TYR J 121 ARG 0.003 0.000 ARG J 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 20) link_NAG-ASN : angle 2.80720 ( 60) link_ALPHA1-6 : bond 0.00498 ( 8) link_ALPHA1-6 : angle 1.45772 ( 24) link_BETA1-4 : bond 0.00420 ( 16) link_BETA1-4 : angle 1.88770 ( 48) link_ALPHA1-2 : bond 0.00075 ( 4) link_ALPHA1-2 : angle 2.71011 ( 12) link_ALPHA1-3 : bond 0.00614 ( 8) link_ALPHA1-3 : angle 2.14279 ( 24) hydrogen bonds : bond 0.04727 ( 656) hydrogen bonds : angle 6.43417 ( 1728) SS BOND : bond 0.00329 ( 44) SS BOND : angle 0.68458 ( 88) covalent geometry : bond 0.00495 (20492) covalent geometry : angle 0.63254 (27824) *********************** 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 298 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 2.067 Fit side-chains REVERT: G 400 ARG cc_start: 0.8518 (ptm-80) cc_final: 0.7868 (ptm160) REVERT: A 62 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7583 (tp-100) REVERT: L 61 ARG cc_start: 0.8843 (ptt-90) cc_final: 0.8460 (ptt-90) REVERT: L 70 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8093 (mm110) REVERT: L 101 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8491 (mm110) REVERT: H 400 ARG cc_start: 0.8527 (ptm-80) cc_final: 0.7869 (ptm160) REVERT: B 62 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7587 (tp-100) REVERT: M 61 ARG cc_start: 0.8843 (ptt-90) cc_final: 0.8459 (ptt-90) REVERT: M 70 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8096 (mm110) REVERT: M 101 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8492 (mm110) REVERT: I 400 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.7853 (ptm160) REVERT: C 62 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7586 (tp-100) REVERT: N 61 ARG cc_start: 0.8847 (ptt-90) cc_final: 0.8465 (ptt-90) REVERT: N 70 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8104 (mm110) REVERT: N 101 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8486 (mm110) REVERT: J 400 ARG cc_start: 0.8493 (ptm-80) cc_final: 0.7854 (ptm160) REVERT: D 62 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7698 (tp-100) REVERT: O 61 ARG cc_start: 0.8849 (ptt-90) cc_final: 0.8539 (ptt-90) REVERT: O 70 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8095 (mm110) REVERT: O 101 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8485 (mm110) outliers start: 44 outliers final: 25 residues processed: 278 average time/residue: 1.2711 time to fit residues: 401.3198 Evaluate side-chains 272 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 56 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 56 THR Chi-restraints excluded: chain M residue 74 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 74 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 175 optimal weight: 0.0020 chunk 238 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 150 optimal weight: 0.0070 chunk 215 optimal weight: 0.0170 chunk 61 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.5446 ------------------------------------------------------------------------------- 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 B 30 ASN B 65 GLN M 6 GLN C 65 GLN N 6 GLN O 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071574 restraints weight = 28112.364| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.18 r_work: 0.2726 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20592 Z= 0.109 Angle : 0.574 7.900 28080 Z= 0.301 Chirality : 0.045 0.179 3196 Planarity : 0.003 0.039 3500 Dihedral : 7.603 60.356 3848 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.25 % Rotamer: Outliers : 1.18 % Allowed : 10.47 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2476 helix: -0.50 (0.85), residues: 28 sheet: 0.33 (0.16), residues: 948 loop : -0.10 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 178 HIS 0.003 0.001 HIS H 274 PHE 0.012 0.002 PHE G 354 TYR 0.012 0.001 TYR G 121 ARG 0.002 0.000 ARG J 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 20) link_NAG-ASN : angle 2.34165 ( 60) link_ALPHA1-6 : bond 0.00634 ( 8) link_ALPHA1-6 : angle 1.33265 ( 24) link_BETA1-4 : bond 0.00537 ( 16) link_BETA1-4 : angle 1.50797 ( 48) link_ALPHA1-2 : bond 0.00451 ( 4) link_ALPHA1-2 : angle 2.19035 ( 12) link_ALPHA1-3 : bond 0.00989 ( 8) link_ALPHA1-3 : angle 1.73567 ( 24) hydrogen bonds : bond 0.03739 ( 656) hydrogen bonds : angle 5.99315 ( 1728) SS BOND : bond 0.00223 ( 44) SS BOND : angle 0.62350 ( 88) covalent geometry : bond 0.00226 (20492) covalent geometry : angle 0.55611 (27824) *********************** 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 290 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 2.186 Fit side-chains REVERT: G 400 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.7759 (ptm160) REVERT: A 62 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7448 (tp-100) REVERT: L 61 ARG cc_start: 0.8858 (ptt-90) cc_final: 0.8465 (ptt-90) REVERT: L 101 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8569 (mm110) REVERT: H 400 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.7762 (ptm160) REVERT: B 62 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7438 (tp-100) REVERT: M 61 ARG cc_start: 0.8857 (ptt-90) cc_final: 0.8470 (ptt-90) REVERT: M 101 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8559 (mm110) REVERT: I 400 ARG cc_start: 0.8403 (ptm-80) cc_final: 0.7755 (ptm160) REVERT: C 62 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7447 (tp-100) REVERT: N 61 ARG cc_start: 0.8858 (ptt-90) cc_final: 0.8473 (ptt-90) REVERT: N 101 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8559 (mm110) REVERT: J 249 LYS cc_start: 0.7008 (tptp) cc_final: 0.6193 (tptt) REVERT: J 400 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.7750 (ptm160) REVERT: D 62 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7658 (tp-100) REVERT: O 61 ARG cc_start: 0.8863 (ptt-90) cc_final: 0.8469 (ptt-90) REVERT: O 101 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8550 (mm110) outliers start: 25 outliers final: 10 residues processed: 273 average time/residue: 1.3742 time to fit residues: 422.0045 Evaluate side-chains 261 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 251 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 70 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 163 optimal weight: 0.0170 chunk 83 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 170 optimal weight: 0.0020 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.4426 ------------------------------------------------------------------------------- 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 D 30 ASN 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 = 0.3359 r_free = 0.3359 target = 0.100654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.072817 restraints weight = 28180.304| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.18 r_work: 0.2777 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20592 Z= 0.103 Angle : 0.553 7.982 28080 Z= 0.288 Chirality : 0.044 0.200 3196 Planarity : 0.003 0.041 3500 Dihedral : 6.928 52.431 3848 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 1.32 % Allowed : 11.18 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2476 helix: -1.61 (0.63), residues: 52 sheet: 0.35 (0.15), residues: 1040 loop : -0.04 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 178 HIS 0.003 0.001 HIS H 274 PHE 0.011 0.001 PHE H 354 TYR 0.012 0.001 TYR I 121 ARG 0.002 0.000 ARG M 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 20) link_NAG-ASN : angle 2.21637 ( 60) link_ALPHA1-6 : bond 0.00653 ( 8) link_ALPHA1-6 : angle 1.40035 ( 24) link_BETA1-4 : bond 0.00501 ( 16) link_BETA1-4 : angle 1.41595 ( 48) link_ALPHA1-2 : bond 0.00415 ( 4) link_ALPHA1-2 : angle 2.17030 ( 12) link_ALPHA1-3 : bond 0.00905 ( 8) link_ALPHA1-3 : angle 1.70589 ( 24) hydrogen bonds : bond 0.03547 ( 656) hydrogen bonds : angle 5.75728 ( 1728) SS BOND : bond 0.00167 ( 44) SS BOND : angle 0.53563 ( 88) covalent geometry : bond 0.00216 (20492) covalent geometry : angle 0.53640 (27824) *********************** 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 293 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 2.103 Fit side-chains REVERT: G 362 MET cc_start: 0.9239 (ptp) cc_final: 0.8971 (ptp) REVERT: G 400 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.7738 (ptm160) REVERT: A 62 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7436 (tp-100) REVERT: L 61 ARG cc_start: 0.8778 (ptt-90) cc_final: 0.8513 (ptt-90) REVERT: L 101 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8570 (mm110) REVERT: H 362 MET cc_start: 0.9239 (ptp) cc_final: 0.8974 (ptp) REVERT: H 400 ARG cc_start: 0.8429 (ptm-80) cc_final: 0.7754 (ptm160) REVERT: B 62 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7453 (tp-100) REVERT: M 61 ARG cc_start: 0.8782 (ptt-90) cc_final: 0.8498 (ptt-90) REVERT: M 101 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8557 (mm110) REVERT: I 362 MET cc_start: 0.9238 (ptp) cc_final: 0.8974 (ptp) REVERT: I 400 ARG cc_start: 0.8375 (ptm-80) cc_final: 0.7727 (ptm160) REVERT: C 62 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7430 (tp-100) REVERT: N 61 ARG cc_start: 0.8785 (ptt-90) cc_final: 0.8502 (ptt-90) REVERT: N 101 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8557 (mm110) REVERT: J 362 MET cc_start: 0.9237 (ptp) cc_final: 0.8969 (ptp) REVERT: J 400 ARG cc_start: 0.8367 (ptm-80) cc_final: 0.7725 (ptm160) REVERT: D 62 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7638 (tp-100) REVERT: O 61 ARG cc_start: 0.8793 (ptt-90) cc_final: 0.8508 (ptt-90) outliers start: 28 outliers final: 15 residues processed: 273 average time/residue: 1.3772 time to fit residues: 425.4810 Evaluate side-chains 265 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 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 I residue 148 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 J residue 148 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 210 optimal weight: 0.0470 chunk 101 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.099701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.071804 restraints weight = 28173.409| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.17 r_work: 0.2759 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20592 Z= 0.125 Angle : 0.568 7.331 28080 Z= 0.296 Chirality : 0.045 0.210 3196 Planarity : 0.003 0.041 3500 Dihedral : 6.891 51.648 3848 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.32 % Allowed : 11.65 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2476 helix: -1.67 (0.63), residues: 52 sheet: 0.46 (0.16), residues: 940 loop : -0.04 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 178 HIS 0.002 0.001 HIS J 274 PHE 0.013 0.002 PHE J 410 TYR 0.012 0.001 TYR H 121 ARG 0.005 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 20) link_NAG-ASN : angle 2.21580 ( 60) link_ALPHA1-6 : bond 0.00580 ( 8) link_ALPHA1-6 : angle 1.42838 ( 24) link_BETA1-4 : bond 0.00440 ( 16) link_BETA1-4 : angle 1.40847 ( 48) link_ALPHA1-2 : bond 0.00327 ( 4) link_ALPHA1-2 : angle 2.21762 ( 12) link_ALPHA1-3 : bond 0.00802 ( 8) link_ALPHA1-3 : angle 1.79205 ( 24) hydrogen bonds : bond 0.03731 ( 656) hydrogen bonds : angle 5.78930 ( 1728) SS BOND : bond 0.00214 ( 44) SS BOND : angle 0.77253 ( 88) covalent geometry : bond 0.00271 (20492) covalent geometry : angle 0.55088 (27824) *********************** 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 290 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 2.076 Fit side-chains REVERT: G 362 MET cc_start: 0.9255 (ptp) cc_final: 0.9037 (ptp) REVERT: G 400 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.7741 (ptm160) REVERT: A 62 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7453 (tp-100) REVERT: A 82 GLU cc_start: 0.8205 (tt0) cc_final: 0.7724 (mm-30) REVERT: L 61 ARG cc_start: 0.8778 (ptt-90) cc_final: 0.8486 (ptt-90) REVERT: L 101 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8593 (mm110) REVERT: H 362 MET cc_start: 0.9248 (ptp) cc_final: 0.9032 (ptp) REVERT: H 400 ARG cc_start: 0.8439 (ptm-80) cc_final: 0.7758 (ptm160) REVERT: B 62 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7469 (tp-100) REVERT: B 82 GLU cc_start: 0.8202 (tt0) cc_final: 0.7603 (mm-30) REVERT: M 61 ARG cc_start: 0.8779 (ptt-90) cc_final: 0.8494 (ptt-90) REVERT: M 101 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8588 (mm110) REVERT: I 362 MET cc_start: 0.9250 (ptp) cc_final: 0.9034 (ptp) REVERT: I 400 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.7744 (ptm160) REVERT: C 62 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7433 (tp-100) REVERT: C 65 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: C 82 GLU cc_start: 0.8195 (tt0) cc_final: 0.7650 (mm-30) REVERT: N 61 ARG cc_start: 0.8781 (ptt-90) cc_final: 0.8496 (ptt-90) REVERT: N 101 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8592 (mm110) REVERT: J 362 MET cc_start: 0.9253 (ptp) cc_final: 0.9035 (ptp) REVERT: J 400 ARG cc_start: 0.8411 (ptm-80) cc_final: 0.7739 (ptm160) REVERT: D 62 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7640 (tp-100) REVERT: D 82 GLU cc_start: 0.8181 (tt0) cc_final: 0.7588 (mm-30) REVERT: O 61 ARG cc_start: 0.8790 (ptt-90) cc_final: 0.8500 (ptt-90) outliers start: 28 outliers final: 19 residues processed: 273 average time/residue: 1.4019 time to fit residues: 433.3654 Evaluate side-chains 277 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 2.336 ------------------------------------------------------------------------------- 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 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 390 LEU 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 28 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 0.0770 chunk 199 optimal weight: 2.9990 chunk 223 optimal weight: 0.0030 chunk 44 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.4348 ------------------------------------------------------------------------------- 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 N 6 GLN N 70 GLN 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 = 0.3364 r_free = 0.3364 target = 0.100968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.073186 restraints weight = 27973.870| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.18 r_work: 0.2787 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20592 Z= 0.101 Angle : 0.551 7.505 28080 Z= 0.285 Chirality : 0.044 0.203 3196 Planarity : 0.003 0.041 3500 Dihedral : 6.589 47.755 3848 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 0.80 % Allowed : 12.92 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2476 helix: -1.67 (0.63), residues: 52 sheet: 0.44 (0.16), residues: 948 loop : 0.02 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 178 HIS 0.002 0.001 HIS H 274 PHE 0.012 0.001 PHE J 410 TYR 0.012 0.001 TYR H 121 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 20) link_NAG-ASN : angle 2.08776 ( 60) link_ALPHA1-6 : bond 0.00654 ( 8) link_ALPHA1-6 : angle 1.39963 ( 24) link_BETA1-4 : bond 0.00508 ( 16) link_BETA1-4 : angle 1.30275 ( 48) link_ALPHA1-2 : bond 0.00415 ( 4) link_ALPHA1-2 : angle 2.11949 ( 12) link_ALPHA1-3 : bond 0.00930 ( 8) link_ALPHA1-3 : angle 1.64765 ( 24) hydrogen bonds : bond 0.03480 ( 656) hydrogen bonds : angle 5.66025 ( 1728) SS BOND : bond 0.00175 ( 44) SS BOND : angle 0.61260 ( 88) covalent geometry : bond 0.00210 (20492) covalent geometry : angle 0.53538 (27824) *********************** 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 279 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 2.110 Fit side-chains REVERT: G 362 MET cc_start: 0.9241 (ptp) cc_final: 0.8986 (ptp) REVERT: G 400 ARG cc_start: 0.8404 (ptm-80) cc_final: 0.7724 (ptm160) REVERT: A 62 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7438 (tp-100) REVERT: A 65 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: A 82 GLU cc_start: 0.8280 (tt0) cc_final: 0.7662 (mm-30) REVERT: L 61 ARG cc_start: 0.8752 (ptt-90) cc_final: 0.8463 (ptt-90) REVERT: H 362 MET cc_start: 0.9235 (ptp) cc_final: 0.8982 (ptp) REVERT: H 400 ARG cc_start: 0.8412 (ptm-80) cc_final: 0.7739 (ptm160) REVERT: B 19 ARG cc_start: 0.9108 (ttt-90) cc_final: 0.8892 (ttt90) REVERT: B 62 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7471 (tp-100) REVERT: B 82 GLU cc_start: 0.8213 (tt0) cc_final: 0.7765 (mm-30) REVERT: M 61 ARG cc_start: 0.8754 (ptt-90) cc_final: 0.8457 (ptt-90) REVERT: I 362 MET cc_start: 0.9237 (ptp) cc_final: 0.8986 (ptp) REVERT: I 400 ARG cc_start: 0.8382 (ptm-80) cc_final: 0.7717 (ptm160) REVERT: C 19 ARG cc_start: 0.9104 (ttt-90) cc_final: 0.8883 (ttt90) REVERT: C 62 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7445 (tp-100) REVERT: C 82 GLU cc_start: 0.8196 (tt0) cc_final: 0.7745 (mm-30) REVERT: N 61 ARG cc_start: 0.8754 (ptt-90) cc_final: 0.8455 (ptt-90) REVERT: J 362 MET cc_start: 0.9240 (ptp) cc_final: 0.8984 (ptp) REVERT: J 400 ARG cc_start: 0.8372 (ptm-80) cc_final: 0.7711 (ptm160) REVERT: D 19 ARG cc_start: 0.9109 (ttt-90) cc_final: 0.8889 (ttt90) REVERT: D 62 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7610 (tp-100) REVERT: D 82 GLU cc_start: 0.8206 (tt0) cc_final: 0.7751 (mm-30) REVERT: O 61 ARG cc_start: 0.8781 (ptt-90) cc_final: 0.8483 (ptt-90) outliers start: 17 outliers final: 11 residues processed: 271 average time/residue: 1.3606 time to fit residues: 415.2819 Evaluate side-chains 269 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain D residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 92 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 235 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 C 65 GLN N 6 GLN N 70 GLN 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 = 0.3345 r_free = 0.3345 target = 0.099653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.071606 restraints weight = 28265.902| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.19 r_work: 0.2754 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20592 Z= 0.137 Angle : 0.577 7.630 28080 Z= 0.298 Chirality : 0.045 0.215 3196 Planarity : 0.003 0.041 3500 Dihedral : 6.726 49.267 3848 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.83 % Favored : 97.01 % Rotamer: Outliers : 0.94 % Allowed : 13.25 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2476 helix: -1.69 (0.62), residues: 52 sheet: 0.57 (0.16), residues: 928 loop : -0.00 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 178 HIS 0.002 0.001 HIS H 274 PHE 0.012 0.002 PHE J 410 TYR 0.012 0.001 TYR H 121 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 20) link_NAG-ASN : angle 2.20503 ( 60) link_ALPHA1-6 : bond 0.00542 ( 8) link_ALPHA1-6 : angle 1.45258 ( 24) link_BETA1-4 : bond 0.00434 ( 16) link_BETA1-4 : angle 1.37731 ( 48) link_ALPHA1-2 : bond 0.00271 ( 4) link_ALPHA1-2 : angle 2.21997 ( 12) link_ALPHA1-3 : bond 0.00799 ( 8) link_ALPHA1-3 : angle 1.84497 ( 24) hydrogen bonds : bond 0.03797 ( 656) hydrogen bonds : angle 5.76310 ( 1728) SS BOND : bond 0.00214 ( 44) SS BOND : angle 0.59963 ( 88) covalent geometry : bond 0.00302 (20492) covalent geometry : angle 0.56018 (27824) *********************** 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 280 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 2.091 Fit side-chains REVERT: G 400 ARG cc_start: 0.8450 (ptm-80) cc_final: 0.7751 (ptm160) REVERT: A 19 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8888 (ttt90) REVERT: A 62 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7488 (tp-100) REVERT: A 82 GLU cc_start: 0.8229 (tt0) cc_final: 0.7797 (mm-30) REVERT: L 61 ARG cc_start: 0.8762 (ptt-90) cc_final: 0.8442 (ptt-90) REVERT: H 400 ARG cc_start: 0.8467 (ptm-80) cc_final: 0.7775 (ptm160) REVERT: B 19 ARG cc_start: 0.9126 (ttt-90) cc_final: 0.8896 (ttt90) REVERT: B 62 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7502 (tp-100) REVERT: B 65 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: B 82 GLU cc_start: 0.8235 (tt0) cc_final: 0.7774 (mm-30) REVERT: M 61 ARG cc_start: 0.8764 (ptt-90) cc_final: 0.8443 (ptt-90) REVERT: I 362 MET cc_start: 0.9252 (ptp) cc_final: 0.9050 (ptp) REVERT: I 400 ARG cc_start: 0.8441 (ptm-80) cc_final: 0.7755 (ptm160) REVERT: C 19 ARG cc_start: 0.9116 (ttt-90) cc_final: 0.8882 (ttt90) REVERT: C 62 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7465 (tp-100) REVERT: C 65 GLN cc_start: 0.7637 (tt0) cc_final: 0.7342 (tt0) REVERT: C 82 GLU cc_start: 0.8244 (tt0) cc_final: 0.7796 (mm-30) REVERT: N 61 ARG cc_start: 0.8761 (ptt-90) cc_final: 0.8438 (ptt-90) REVERT: J 362 MET cc_start: 0.9255 (ptp) cc_final: 0.9051 (ptp) REVERT: J 400 ARG cc_start: 0.8440 (ptm-80) cc_final: 0.7753 (ptm160) REVERT: D 19 ARG cc_start: 0.9115 (ttt-90) cc_final: 0.8884 (ttt90) REVERT: D 62 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7604 (tp-100) REVERT: D 82 GLU cc_start: 0.8219 (tt0) cc_final: 0.7771 (mm-30) REVERT: O 61 ARG cc_start: 0.8788 (ptt-90) cc_final: 0.8464 (ptt-90) outliers start: 20 outliers final: 19 residues processed: 266 average time/residue: 1.3608 time to fit residues: 410.1913 Evaluate side-chains 276 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 2.416 ------------------------------------------------------------------------------- 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 390 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 108 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 229 optimal weight: 0.0670 chunk 50 optimal weight: 0.0170 chunk 200 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 N 6 GLN N 70 GLN 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 = 0.3350 r_free = 0.3350 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.072103 restraints weight = 27912.502| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.18 r_work: 0.2740 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20592 Z= 0.119 Angle : 0.563 7.556 28080 Z= 0.292 Chirality : 0.045 0.210 3196 Planarity : 0.003 0.041 3500 Dihedral : 6.621 47.836 3848 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 0.94 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2476 helix: -1.70 (0.61), residues: 52 sheet: 0.55 (0.16), residues: 936 loop : -0.03 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 178 HIS 0.002 0.001 HIS I 274 PHE 0.012 0.001 PHE J 410 TYR 0.012 0.001 TYR H 121 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 20) link_NAG-ASN : angle 2.14188 ( 60) link_ALPHA1-6 : bond 0.00578 ( 8) link_ALPHA1-6 : angle 1.43786 ( 24) link_BETA1-4 : bond 0.00467 ( 16) link_BETA1-4 : angle 1.32812 ( 48) link_ALPHA1-2 : bond 0.00319 ( 4) link_ALPHA1-2 : angle 2.15991 ( 12) link_ALPHA1-3 : bond 0.00844 ( 8) link_ALPHA1-3 : angle 1.75057 ( 24) hydrogen bonds : bond 0.03674 ( 656) hydrogen bonds : angle 5.71758 ( 1728) SS BOND : bond 0.00192 ( 44) SS BOND : angle 0.54736 ( 88) covalent geometry : bond 0.00257 (20492) covalent geometry : angle 0.54772 (27824) *********************** 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 275 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 2.021 Fit side-chains REVERT: G 400 ARG cc_start: 0.8433 (ptm-80) cc_final: 0.7728 (ptm160) REVERT: A 19 ARG cc_start: 0.9116 (ttt-90) cc_final: 0.8871 (ttt90) REVERT: A 62 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7467 (tp-100) REVERT: A 65 GLN cc_start: 0.7541 (tt0) cc_final: 0.7292 (tt0) REVERT: A 82 GLU cc_start: 0.8255 (tt0) cc_final: 0.7807 (mm-30) REVERT: L 61 ARG cc_start: 0.8756 (ptt-90) cc_final: 0.8432 (ptt-90) REVERT: H 400 ARG cc_start: 0.8443 (ptm-80) cc_final: 0.7747 (ptm160) REVERT: B 19 ARG cc_start: 0.9127 (ttt-90) cc_final: 0.8889 (ttt90) REVERT: B 62 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7546 (tp-100) REVERT: B 82 GLU cc_start: 0.8249 (tt0) cc_final: 0.7804 (mm-30) REVERT: M 61 ARG cc_start: 0.8754 (ptt-90) cc_final: 0.8428 (ptt-90) REVERT: I 400 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.7731 (ptm160) REVERT: C 19 ARG cc_start: 0.9120 (ttt-90) cc_final: 0.8879 (ttt90) REVERT: C 62 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7468 (tp-100) REVERT: C 65 GLN cc_start: 0.7627 (tt0) cc_final: 0.7313 (tt0) REVERT: C 82 GLU cc_start: 0.8258 (tt0) cc_final: 0.7798 (mm-30) REVERT: N 61 ARG cc_start: 0.8754 (ptt-90) cc_final: 0.8425 (ptt-90) REVERT: J 400 ARG cc_start: 0.8410 (ptm-80) cc_final: 0.7721 (ptm160) REVERT: D 19 ARG cc_start: 0.9125 (ttt-90) cc_final: 0.8879 (ttt90) REVERT: D 62 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7607 (tp-100) REVERT: D 82 GLU cc_start: 0.8249 (tt0) cc_final: 0.7789 (mm-30) REVERT: O 61 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8434 (ptt-90) outliers start: 20 outliers final: 15 residues processed: 265 average time/residue: 1.2973 time to fit residues: 388.9530 Evaluate side-chains 269 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR 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 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 390 LEU 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 D residue 34 LEU 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 20 optimal weight: 0.0870 chunk 35 optimal weight: 0.0370 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 172 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 181 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 overall best weight: 0.1654 ------------------------------------------------------------------------------- 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 O 6 GLN O 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.076346 restraints weight = 28027.657| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.18 r_work: 0.2826 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20592 Z= 0.091 Angle : 0.536 8.234 28080 Z= 0.276 Chirality : 0.044 0.193 3196 Planarity : 0.003 0.040 3500 Dihedral : 5.950 44.139 3848 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.63 % Favored : 97.21 % Rotamer: Outliers : 0.57 % Allowed : 14.01 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2476 helix: -1.64 (0.62), residues: 52 sheet: 0.35 (0.16), residues: 984 loop : 0.11 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 178 HIS 0.002 0.000 HIS H 274 PHE 0.012 0.001 PHE I 354 TYR 0.011 0.001 TYR J 121 ARG 0.005 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 20) link_NAG-ASN : angle 1.82145 ( 60) link_ALPHA1-6 : bond 0.00774 ( 8) link_ALPHA1-6 : angle 1.33464 ( 24) link_BETA1-4 : bond 0.00521 ( 16) link_BETA1-4 : angle 1.12974 ( 48) link_ALPHA1-2 : bond 0.00527 ( 4) link_ALPHA1-2 : angle 1.88374 ( 12) link_ALPHA1-3 : bond 0.01087 ( 8) link_ALPHA1-3 : angle 1.42475 ( 24) hydrogen bonds : bond 0.03136 ( 656) hydrogen bonds : angle 5.42664 ( 1728) SS BOND : bond 0.00174 ( 44) SS BOND : angle 0.52903 ( 88) covalent geometry : bond 0.00188 (20492) covalent geometry : angle 0.52385 (27824) ********************** 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 297 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 285 time to evaluate : 2.114 Fit side-chains REVERT: G 400 ARG cc_start: 0.8337 (ptm-80) cc_final: 0.7661 (ptm160) REVERT: A 19 ARG cc_start: 0.9083 (ttt-90) cc_final: 0.8853 (ttt-90) REVERT: A 62 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7398 (tp-100) REVERT: A 65 GLN cc_start: 0.7585 (tt0) cc_final: 0.7324 (tt0) REVERT: A 82 GLU cc_start: 0.8236 (tt0) cc_final: 0.7748 (mm-30) REVERT: L 61 ARG cc_start: 0.8706 (ptt-90) cc_final: 0.8405 (ptt-90) REVERT: H 400 ARG cc_start: 0.8360 (ptm-80) cc_final: 0.7677 (ptm160) REVERT: B 19 ARG cc_start: 0.9101 (ttt-90) cc_final: 0.8845 (ttt90) REVERT: B 62 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7375 (tp-100) REVERT: B 82 GLU cc_start: 0.8227 (tt0) cc_final: 0.7753 (mm-30) REVERT: M 61 ARG cc_start: 0.8705 (ptt-90) cc_final: 0.8403 (ptt-90) REVERT: I 400 ARG cc_start: 0.8319 (ptm-80) cc_final: 0.7657 (ptm160) REVERT: C 19 ARG cc_start: 0.9106 (ttt-90) cc_final: 0.8843 (ttt90) REVERT: C 62 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7429 (tp-100) REVERT: C 65 GLN cc_start: 0.7567 (tt0) cc_final: 0.7292 (tt0) REVERT: C 82 GLU cc_start: 0.8236 (tt0) cc_final: 0.7765 (mm-30) REVERT: N 61 ARG cc_start: 0.8704 (ptt-90) cc_final: 0.8398 (ptt-90) REVERT: J 400 ARG cc_start: 0.8313 (ptm-80) cc_final: 0.7654 (ptm160) REVERT: D 19 ARG cc_start: 0.9099 (ttt-90) cc_final: 0.8835 (ttt90) REVERT: D 62 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7587 (tp-100) REVERT: D 82 GLU cc_start: 0.8219 (tt0) cc_final: 0.7755 (mm-30) REVERT: O 61 ARG cc_start: 0.8740 (ptt-90) cc_final: 0.8434 (ptt-90) outliers start: 12 outliers final: 9 residues processed: 289 average time/residue: 1.1979 time to fit residues: 394.7749 Evaluate side-chains 260 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 251 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 247 THR 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 B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 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 42 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN B 65 GLN M 6 GLN I 220 ASN N 6 GLN J 220 ASN O 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.070842 restraints weight = 28236.351| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.18 r_work: 0.2716 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2468 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= 0.176 Angle : 0.600 7.092 28080 Z= 0.311 Chirality : 0.046 0.226 3196 Planarity : 0.003 0.042 3500 Dihedral : 6.569 46.049 3848 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.97 % Rotamer: Outliers : 0.71 % Allowed : 14.53 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2476 helix: -1.64 (0.61), residues: 52 sheet: 0.34 (0.15), residues: 1064 loop : 0.10 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 178 HIS 0.002 0.001 HIS G 184 PHE 0.013 0.002 PHE J 410 TYR 0.011 0.002 TYR H 121 ARG 0.005 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 20) link_NAG-ASN : angle 2.24660 ( 60) link_ALPHA1-6 : bond 0.00475 ( 8) link_ALPHA1-6 : angle 1.53847 ( 24) link_BETA1-4 : bond 0.00383 ( 16) link_BETA1-4 : angle 1.33952 ( 48) link_ALPHA1-2 : bond 0.00135 ( 4) link_ALPHA1-2 : angle 2.17952 ( 12) link_ALPHA1-3 : bond 0.00701 ( 8) link_ALPHA1-3 : angle 1.90496 ( 24) hydrogen bonds : bond 0.03993 ( 656) hydrogen bonds : angle 5.80407 ( 1728) SS BOND : bond 0.00253 ( 44) SS BOND : angle 0.61701 ( 88) covalent geometry : bond 0.00399 (20492) covalent geometry : angle 0.58416 (27824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16945.18 seconds wall clock time: 290 minutes 28.42 seconds (17428.42 seconds total)