Starting phenix.real_space_refine on Sat May 17 05:05:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxy_29548/05_2025/8fxy_29548_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxy_29548/05_2025/8fxy_29548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxy_29548/05_2025/8fxy_29548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxy_29548/05_2025/8fxy_29548.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxy_29548/05_2025/8fxy_29548_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxy_29548/05_2025/8fxy_29548_trim.cif" } resolution = 3.34 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 9456 2.51 5 N 2496 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15042 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "D" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "E" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "F" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "G" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "I" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "J" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "K" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1564 Classifications: {'peptide': 196} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "L" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 901 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.93, per 1000 atoms: 0.59 Number of scatterers: 15042 At special positions: 0 Unit cell: (177.1, 163.9, 62.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 2952 8.00 N 2496 7.00 C 9456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS K 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS B 4 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS D 4 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 184 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS F 4 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 184 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 85 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 109 " - pdb=" SG CYS I 4 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 184 " distance=2.04 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 85 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 104 " - pdb=" SG CYS I 136 " distance=2.03 Simple disulfide: pdb=" SG CYS I 109 " - pdb=" SG CYS K 4 " distance=2.03 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 184 " distance=2.04 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 85 " distance=2.03 Simple disulfide: pdb=" SG CYS K 35 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 104 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 184 " distance=2.04 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 201 " - " ASN A 28 " " NAG A 203 " - " ASN A 58 " " NAG B 201 " - " ASN B 28 " " NAG B 203 " - " ASN B 58 " " NAG D 201 " - " ASN D 28 " " NAG D 203 " - " ASN D 58 " " NAG F 201 " - " ASN F 28 " " NAG F 203 " - " ASN F 58 " " NAG I 201 " - " ASN I 28 " " NAG I 203 " - " ASN I 58 " " NAG K 201 " - " ASN K 28 " " NAG K 203 " - " ASN K 58 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 5.9% alpha, 55.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'H' and resid 24 through 26 No H-bonds generated for 'chain 'H' and resid 24 through 26' Processing helix chain 'H' and resid 54 through 58 Processing helix chain 'H' and resid 76 through 80 removed outlier: 4.224A pdb=" N LYS H 80 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 76 through 80 removed outlier: 4.134A pdb=" N LYS C 80 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 54 through 58 Processing helix chain 'E' and resid 76 through 80 removed outlier: 4.058A pdb=" N LYS E 80 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 54 through 58 Processing helix chain 'G' and resid 76 through 80 removed outlier: 4.094A pdb=" N LYS G 80 " --> pdb=" O ILE G 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 170 Processing helix chain 'J' and resid 24 through 26 No H-bonds generated for 'chain 'J' and resid 24 through 26' Processing helix chain 'J' and resid 54 through 58 Processing helix chain 'J' and resid 76 through 80 removed outlier: 4.181A pdb=" N LYS J 80 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 170 removed outlier: 3.547A pdb=" N ARG K 170 " --> pdb=" O TYR K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 26 No H-bonds generated for 'chain 'L' and resid 24 through 26' Processing helix chain 'L' and resid 54 through 58 Processing helix chain 'L' and resid 76 through 80 removed outlier: 4.251A pdb=" N LYS L 80 " --> pdb=" O ILE L 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.784A pdb=" N ASP A 194 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 73 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N SER A 172 " --> pdb=" O HIS H 99 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS H 99 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY A 174 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG H 97 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 89 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS H 99 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 3 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 106 " --> pdb=" O ILE H 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.784A pdb=" N ASP A 194 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 73 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N SER A 172 " --> pdb=" O HIS H 99 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS H 99 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY A 174 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG H 97 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 89 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS H 99 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU H 28 " --> pdb=" O TYR H 44 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR H 44 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL H 30 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU H 42 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP H 32 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU H 42 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.681A pdb=" N MET A 62 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 97 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 98 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR A 131 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 100 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASN A 133 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 102 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 132 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.681A pdb=" N MET A 62 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 97 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 98 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR A 131 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 100 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASN A 133 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 102 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.731A pdb=" N ASP B 194 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 73 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N SER B 172 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N HIS C 99 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY B 174 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 97 " --> pdb=" O HIS C 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS C 89 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 99 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 106 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.731A pdb=" N ASP B 194 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 73 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N SER B 172 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N HIS C 99 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY B 174 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 97 " --> pdb=" O HIS C 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS C 89 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 99 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 28 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR C 44 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 30 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU C 42 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 32 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 42 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 40 removed outlier: 6.910A pdb=" N ILE B 98 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 131 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 100 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN B 133 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 102 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 132 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 40 removed outlier: 6.910A pdb=" N ILE B 98 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 131 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 100 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN B 133 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 102 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 14 Processing sheet with id=AB2, first strand: chain 'D' and resid 194 through 195 removed outlier: 3.698A pdb=" N ASP D 194 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 73 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N SER D 172 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS E 99 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY D 174 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG E 97 " --> pdb=" O HIS E 89 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS E 89 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS E 99 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 106 " --> pdb=" O ILE E 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 194 through 195 removed outlier: 3.698A pdb=" N ASP D 194 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 73 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N SER D 172 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS E 99 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY D 174 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG E 97 " --> pdb=" O HIS E 89 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS E 89 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS E 99 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 28 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TYR E 44 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL E 30 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU E 42 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP E 32 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU E 42 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.671A pdb=" N MET D 62 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN D 97 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 98 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR D 131 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 100 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN D 133 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE D 102 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE D 132 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.671A pdb=" N MET D 62 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN D 97 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 98 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR D 131 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 100 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN D 133 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE D 102 " --> pdb=" O ASN D 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AB7, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.720A pdb=" N ASP F 194 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 73 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N SER F 172 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS G 99 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY F 174 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG G 97 " --> pdb=" O HIS G 89 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS G 89 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS G 99 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 106 " --> pdb=" O ILE G 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.720A pdb=" N ASP F 194 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 73 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N SER F 172 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS G 99 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY F 174 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG G 97 " --> pdb=" O HIS G 89 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS G 89 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS G 99 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU G 28 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR G 44 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL G 30 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU G 42 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP G 32 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU G 42 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 36 through 40 removed outlier: 3.549A pdb=" N MET F 62 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN F 97 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE F 98 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR F 131 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 100 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN F 133 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE F 102 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE F 132 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 36 through 40 removed outlier: 3.549A pdb=" N MET F 62 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN F 97 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE F 98 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR F 131 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 100 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN F 133 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE F 102 " --> pdb=" O ASN F 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 11 through 14 Processing sheet with id=AC3, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.628A pdb=" N ASP I 194 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU I 73 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N SER I 172 " --> pdb=" O HIS J 99 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HIS J 99 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY I 174 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG J 97 " --> pdb=" O HIS J 89 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS J 89 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS J 99 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU J 1 " --> pdb=" O ASN J 102 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER J 106 " --> pdb=" O ILE J 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.628A pdb=" N ASP I 194 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU I 73 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N SER I 172 " --> pdb=" O HIS J 99 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HIS J 99 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY I 174 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG J 97 " --> pdb=" O HIS J 89 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS J 89 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS J 99 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU J 28 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR J 44 " --> pdb=" O LEU J 28 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL J 30 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU J 42 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP J 32 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU J 42 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 36 through 40 removed outlier: 3.782A pdb=" N MET I 62 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN I 97 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE I 98 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR I 131 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL I 100 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN I 133 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE I 102 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE I 132 " --> pdb=" O LYS I 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 36 through 40 removed outlier: 3.782A pdb=" N MET I 62 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN I 97 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE I 98 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N THR I 131 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL I 100 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN I 133 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE I 102 " --> pdb=" O ASN I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 11 through 14 Processing sheet with id=AC8, first strand: chain 'K' and resid 194 through 195 removed outlier: 3.744A pdb=" N ASP K 194 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 73 " --> pdb=" O ASP K 194 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER K 172 " --> pdb=" O HIS L 99 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS L 99 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLY K 174 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG L 97 " --> pdb=" O HIS L 89 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS L 89 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS L 99 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER L 106 " --> pdb=" O ILE L 3 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 194 through 195 removed outlier: 3.744A pdb=" N ASP K 194 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 73 " --> pdb=" O ASP K 194 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER K 172 " --> pdb=" O HIS L 99 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS L 99 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLY K 174 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG L 97 " --> pdb=" O HIS L 89 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS L 89 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS L 99 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU L 28 " --> pdb=" O TYR L 44 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR L 44 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL L 30 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU L 42 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP L 32 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU L 42 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 36 through 40 removed outlier: 3.569A pdb=" N MET K 62 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN K 97 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE K 98 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N THR K 131 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL K 100 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN K 133 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE K 102 " --> pdb=" O ASN K 133 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE K 132 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 36 through 40 removed outlier: 3.569A pdb=" N MET K 62 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN K 97 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE K 98 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N THR K 131 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL K 100 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN K 133 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE K 102 " --> pdb=" O ASN K 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 11 through 14 709 hydrogen bonds defined for protein. 1782 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: 5.04 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4872 1.35 - 1.47: 3749 1.47 - 1.59: 6523 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 15354 Sorted by residual: bond pdb=" C1 NAG F 201 " pdb=" O5 NAG F 201 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C1 NAG D 201 " pdb=" O5 NAG D 201 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG B 201 " pdb=" O5 NAG B 201 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C1 NAG K 201 " pdb=" O5 NAG K 201 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C1 NAG D 203 " pdb=" O5 NAG D 203 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 15349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 19592 1.12 - 2.24: 941 2.24 - 3.36: 177 3.36 - 4.47: 55 4.47 - 5.59: 13 Bond angle restraints: 20778 Sorted by residual: angle pdb=" N MET B 107 " pdb=" CA MET B 107 " pdb=" CB MET B 107 " ideal model delta sigma weight residual 114.17 109.61 4.56 1.14e+00 7.69e-01 1.60e+01 angle pdb=" N MET I 107 " pdb=" CA MET I 107 " pdb=" CB MET I 107 " ideal model delta sigma weight residual 114.17 109.63 4.54 1.14e+00 7.69e-01 1.59e+01 angle pdb=" N MET A 107 " pdb=" CA MET A 107 " pdb=" CB MET A 107 " ideal model delta sigma weight residual 114.17 109.63 4.54 1.14e+00 7.69e-01 1.58e+01 angle pdb=" N MET F 107 " pdb=" CA MET F 107 " pdb=" CB MET F 107 " ideal model delta sigma weight residual 114.17 109.71 4.46 1.14e+00 7.69e-01 1.53e+01 angle pdb=" N ILE F 149 " pdb=" CA ILE F 149 " pdb=" C ILE F 149 " ideal model delta sigma weight residual 106.21 110.36 -4.15 1.07e+00 8.73e-01 1.51e+01 ... (remaining 20773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 8908 17.04 - 34.08: 455 34.08 - 51.12: 115 51.12 - 68.16: 34 68.16 - 85.20: 4 Dihedral angle restraints: 9516 sinusoidal: 4092 harmonic: 5424 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -39.48 -46.52 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CB CYS E 15 " pdb=" SG CYS E 15 " pdb=" SG CYS E 85 " pdb=" CB CYS E 85 " ideal model delta sinusoidal sigma weight residual -86.00 -40.71 -45.29 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS L 15 " pdb=" SG CYS L 15 " pdb=" SG CYS L 85 " pdb=" CB CYS L 85 " ideal model delta sinusoidal sigma weight residual -86.00 -41.32 -44.68 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 9513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1501 0.028 - 0.057: 477 0.057 - 0.085: 172 0.085 - 0.113: 171 0.113 - 0.142: 25 Chirality restraints: 2346 Sorted by residual: chirality pdb=" CA ILE B 27 " pdb=" N ILE B 27 " pdb=" C ILE B 27 " pdb=" CB ILE B 27 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE D 27 " pdb=" N ILE D 27 " pdb=" C ILE D 27 " pdb=" CB ILE D 27 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE F 27 " pdb=" N ILE F 27 " pdb=" C ILE F 27 " pdb=" CB ILE F 27 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 2343 not shown) Planarity restraints: 2646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS I 4 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO I 5 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO I 5 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 5 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 13 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO G 14 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 13 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO J 14 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO J 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 14 " -0.021 5.00e-02 4.00e+02 ... (remaining 2643 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 412 2.67 - 3.23: 15106 3.23 - 3.79: 20806 3.79 - 4.34: 29970 4.34 - 4.90: 49049 Nonbonded interactions: 115343 Sorted by model distance: nonbonded pdb=" O CYS B 109 " pdb=" N THR D 2 " model vdw 2.117 3.120 nonbonded pdb=" O CYS I 109 " pdb=" N THR K 2 " model vdw 2.135 3.120 nonbonded pdb=" OG SER C 20 " pdb=" OE1 GLN C 21 " model vdw 2.156 3.040 nonbonded pdb=" OG SER E 20 " pdb=" OE1 GLN E 21 " model vdw 2.159 3.040 nonbonded pdb=" OG SER L 20 " pdb=" OE1 GLN L 21 " model vdw 2.160 3.040 ... (remaining 115338 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 1.250 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.980 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 : 0.003 0.025 15396 Z= 0.153 Angle : 0.601 5.592 20874 Z= 0.343 Chirality : 0.041 0.142 2346 Planarity : 0.003 0.039 2634 Dihedral : 11.057 85.195 5934 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 38.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 3.08 % Allowed : 9.02 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.09 (0.20), residues: 1812 helix: None (None), residues: 0 sheet: 0.10 (0.19), residues: 804 loop : -2.82 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 32 HIS 0.003 0.001 HIS L 99 PHE 0.009 0.001 PHE A 185 TYR 0.012 0.001 TYR B 53 ARG 0.002 0.000 ARG I 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 2.38282 ( 36) hydrogen bonds : bond 0.12850 ( 439) hydrogen bonds : angle 6.06068 ( 1782) SS BOND : bond 0.00387 ( 30) SS BOND : angle 1.44572 ( 60) covalent geometry : bond 0.00295 (15354) covalent geometry : angle 0.58888 (20778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7124 (tmm) cc_final: 0.6643 (tmm) REVERT: A 169 MET cc_start: 0.7041 (mmp) cc_final: 0.6748 (mmp) REVERT: A 183 GLN cc_start: 0.3354 (OUTLIER) cc_final: 0.3063 (tp40) REVERT: H 90 LYS cc_start: 0.8104 (tptt) cc_final: 0.7858 (tptt) REVERT: H 101 MET cc_start: 0.7307 (tpp) cc_final: 0.6947 (tpp) REVERT: B 32 MET cc_start: 0.7225 (tmm) cc_final: 0.6747 (tmm) REVERT: B 40 SER cc_start: 0.8217 (m) cc_final: 0.8007 (p) REVERT: B 49 VAL cc_start: 0.8305 (p) cc_final: 0.8041 (t) REVERT: B 101 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8206 (m) REVERT: B 113 LYS cc_start: 0.6264 (mmtm) cc_final: 0.5246 (tttm) REVERT: B 183 GLN cc_start: 0.3602 (OUTLIER) cc_final: 0.3189 (tm-30) REVERT: D 32 MET cc_start: 0.7273 (tmm) cc_final: 0.6976 (tmm) REVERT: D 38 SER cc_start: 0.8450 (m) cc_final: 0.8237 (m) REVERT: D 73 GLU cc_start: 0.6475 (pm20) cc_final: 0.6261 (pm20) REVERT: D 103 THR cc_start: 0.7950 (m) cc_final: 0.7693 (t) REVERT: D 107 MET cc_start: 0.7058 (tpt) cc_final: 0.6805 (tpt) REVERT: D 117 ASP cc_start: 0.7748 (p0) cc_final: 0.7417 (p0) REVERT: D 126 SER cc_start: 0.8154 (t) cc_final: 0.7727 (p) REVERT: D 133 ASN cc_start: 0.8318 (m-40) cc_final: 0.8023 (m-40) REVERT: D 165 SER cc_start: 0.8334 (m) cc_final: 0.8016 (p) REVERT: D 172 SER cc_start: 0.8305 (t) cc_final: 0.7976 (p) REVERT: E 58 MET cc_start: 0.7099 (mmt) cc_final: 0.6606 (mmt) REVERT: E 101 MET cc_start: 0.7305 (tpp) cc_final: 0.6957 (tpp) REVERT: F 12 TYR cc_start: 0.7148 (m-10) cc_final: 0.6749 (m-10) REVERT: F 32 MET cc_start: 0.6851 (tmm) cc_final: 0.6407 (tmm) REVERT: F 82 SER cc_start: 0.8467 (p) cc_final: 0.8245 (p) REVERT: F 101 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8376 (m) REVERT: F 115 ASP cc_start: 0.7604 (t0) cc_final: 0.7181 (t0) REVERT: F 158 ASP cc_start: 0.7915 (m-30) cc_final: 0.7691 (m-30) REVERT: F 165 SER cc_start: 0.8464 (m) cc_final: 0.8078 (p) REVERT: G 0 MET cc_start: 0.2301 (mmt) cc_final: 0.2091 (mmt) REVERT: G 58 MET cc_start: 0.7333 (mmt) cc_final: 0.7113 (mmt) REVERT: G 64 ASP cc_start: 0.7158 (t0) cc_final: 0.6901 (t0) REVERT: I 32 MET cc_start: 0.6842 (tmm) cc_final: 0.6556 (tmm) REVERT: I 40 SER cc_start: 0.8246 (m) cc_final: 0.7929 (p) REVERT: I 49 VAL cc_start: 0.8212 (p) cc_final: 0.8011 (t) REVERT: I 101 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8208 (m) REVERT: I 113 LYS cc_start: 0.6234 (mmtm) cc_final: 0.5135 (tttp) REVERT: I 126 SER cc_start: 0.8432 (t) cc_final: 0.8174 (p) REVERT: I 140 VAL cc_start: 0.7388 (t) cc_final: 0.7015 (p) REVERT: I 165 SER cc_start: 0.8368 (m) cc_final: 0.8106 (p) REVERT: I 172 SER cc_start: 0.8291 (t) cc_final: 0.8033 (p) REVERT: I 183 GLN cc_start: 0.3214 (OUTLIER) cc_final: 0.2897 (tm-30) REVERT: J 8 ASN cc_start: 0.6835 (t0) cc_final: 0.6385 (m-40) REVERT: J 69 THR cc_start: 0.7860 (m) cc_final: 0.7655 (p) REVERT: K 20 THR cc_start: 0.8128 (t) cc_final: 0.7681 (p) REVERT: K 103 THR cc_start: 0.7959 (m) cc_final: 0.7597 (t) REVERT: K 126 SER cc_start: 0.8400 (t) cc_final: 0.7842 (p) REVERT: K 133 ASN cc_start: 0.8096 (m-40) cc_final: 0.7882 (m-40) REVERT: K 165 SER cc_start: 0.8505 (m) cc_final: 0.8225 (p) REVERT: K 172 SER cc_start: 0.8412 (t) cc_final: 0.8138 (p) outliers start: 52 outliers final: 19 residues processed: 395 average time/residue: 0.2205 time to fit residues: 134.7655 Evaluate side-chains 352 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 183 GLN Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN H 37 ASN C 37 ASN C 89 HIS ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 89 HIS F 45 ASN F 133 ASN F 183 GLN G 37 ASN I 97 ASN J 37 ASN J 89 HIS J 99 HIS K 183 GLN L 37 ASN L 89 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.162391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139135 restraints weight = 21608.197| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.65 r_work: 0.3618 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15396 Z= 0.302 Angle : 0.871 14.413 20874 Z= 0.448 Chirality : 0.053 0.173 2346 Planarity : 0.006 0.069 2634 Dihedral : 9.142 84.481 2416 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 5.16 % Allowed : 17.44 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.19 (0.20), residues: 1812 helix: None (None), residues: 0 sheet: 0.01 (0.18), residues: 828 loop : -2.94 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 32 HIS 0.009 0.002 HIS C 99 PHE 0.015 0.003 PHE B 177 TYR 0.025 0.002 TYR B 53 ARG 0.004 0.001 ARG H 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 12) link_NAG-ASN : angle 3.28951 ( 36) hydrogen bonds : bond 0.04838 ( 439) hydrogen bonds : angle 5.29694 ( 1782) SS BOND : bond 0.00720 ( 30) SS BOND : angle 2.70375 ( 60) covalent geometry : bond 0.00699 (15354) covalent geometry : angle 0.85020 (20778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 358 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7309 (m-10) cc_final: 0.7039 (m-10) REVERT: A 32 MET cc_start: 0.7428 (tmm) cc_final: 0.6853 (tmm) REVERT: A 169 MET cc_start: 0.7060 (mmp) cc_final: 0.6717 (mmp) REVERT: B 32 MET cc_start: 0.7521 (tmm) cc_final: 0.6777 (tmm) REVERT: B 37 MET cc_start: 0.8356 (ppp) cc_final: 0.8150 (ptm) REVERT: B 49 VAL cc_start: 0.8298 (p) cc_final: 0.8029 (t) REVERT: B 101 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8012 (p) REVERT: D 32 MET cc_start: 0.7595 (tmm) cc_final: 0.7335 (tmm) REVERT: D 117 ASP cc_start: 0.7589 (p0) cc_final: 0.7208 (p0) REVERT: D 165 SER cc_start: 0.8413 (m) cc_final: 0.8136 (p) REVERT: D 172 SER cc_start: 0.8176 (t) cc_final: 0.7939 (p) REVERT: E 58 MET cc_start: 0.7291 (mmt) cc_final: 0.6808 (mmt) REVERT: E 101 MET cc_start: 0.7298 (tpp) cc_final: 0.7025 (tpp) REVERT: F 32 MET cc_start: 0.7216 (tmm) cc_final: 0.6702 (tmm) REVERT: F 108 ASN cc_start: 0.8181 (m-40) cc_final: 0.7807 (m-40) REVERT: F 117 ASP cc_start: 0.7867 (p0) cc_final: 0.7450 (p0) REVERT: F 158 ASP cc_start: 0.7939 (m-30) cc_final: 0.7631 (m-30) REVERT: F 161 LEU cc_start: 0.8241 (tp) cc_final: 0.8035 (mt) REVERT: F 165 SER cc_start: 0.8532 (m) cc_final: 0.8108 (p) REVERT: G 64 ASP cc_start: 0.7538 (t0) cc_final: 0.7207 (t0) REVERT: G 101 MET cc_start: 0.7556 (tpp) cc_final: 0.7335 (tpp) REVERT: I 32 MET cc_start: 0.7216 (tmm) cc_final: 0.6435 (tmm) REVERT: I 37 MET cc_start: 0.8364 (ppp) cc_final: 0.8009 (ptm) REVERT: I 40 SER cc_start: 0.8017 (m) cc_final: 0.7792 (p) REVERT: I 49 VAL cc_start: 0.8194 (p) cc_final: 0.7885 (m) REVERT: I 101 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8081 (p) REVERT: I 113 LYS cc_start: 0.6214 (mmtm) cc_final: 0.5368 (ttmm) REVERT: I 131 THR cc_start: 0.7963 (m) cc_final: 0.7550 (p) REVERT: I 165 SER cc_start: 0.8483 (m) cc_final: 0.8179 (p) REVERT: J 8 ASN cc_start: 0.6879 (t0) cc_final: 0.6478 (m-40) REVERT: J 69 THR cc_start: 0.8093 (m) cc_final: 0.7691 (p) REVERT: J 107 VAL cc_start: 0.5445 (OUTLIER) cc_final: 0.5244 (t) REVERT: K 115 ASP cc_start: 0.7407 (t0) cc_final: 0.7120 (t0) REVERT: K 117 ASP cc_start: 0.7525 (p0) cc_final: 0.7275 (p0) REVERT: K 126 SER cc_start: 0.8386 (t) cc_final: 0.8153 (p) REVERT: K 129 ASP cc_start: 0.7492 (p0) cc_final: 0.7275 (p0) REVERT: K 165 SER cc_start: 0.8675 (m) cc_final: 0.8414 (p) outliers start: 87 outliers final: 50 residues processed: 412 average time/residue: 0.2134 time to fit residues: 137.8128 Evaluate side-chains 393 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 340 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 21 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 183 GLN B 89 GLN B 97 ASN D 89 GLN D 97 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 97 ASN I 123 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.163331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.140124 restraints weight = 21585.954| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.66 r_work: 0.3641 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15396 Z= 0.212 Angle : 0.766 13.423 20874 Z= 0.395 Chirality : 0.049 0.191 2346 Planarity : 0.005 0.071 2634 Dihedral : 7.552 57.390 2402 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 4.69 % Allowed : 21.12 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 2.08 % 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: -2.27 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.14 (0.19), residues: 786 loop : -2.79 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 13 HIS 0.005 0.001 HIS L 99 PHE 0.027 0.002 PHE A 185 TYR 0.020 0.002 TYR K 25 ARG 0.004 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 12) link_NAG-ASN : angle 2.68802 ( 36) hydrogen bonds : bond 0.04246 ( 439) hydrogen bonds : angle 5.08946 ( 1782) SS BOND : bond 0.00665 ( 30) SS BOND : angle 2.60240 ( 60) covalent geometry : bond 0.00485 (15354) covalent geometry : angle 0.74670 (20778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 329 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7455 (tmm) cc_final: 0.6980 (tmm) REVERT: A 169 MET cc_start: 0.6971 (mmp) cc_final: 0.6769 (mmp) REVERT: A 183 GLN cc_start: 0.2647 (OUTLIER) cc_final: 0.1697 (tp-100) REVERT: B 12 TYR cc_start: 0.7136 (m-10) cc_final: 0.6665 (m-10) REVERT: B 32 MET cc_start: 0.7586 (tmm) cc_final: 0.6846 (tmm) REVERT: B 91 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 101 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 114 TYR cc_start: 0.8600 (t80) cc_final: 0.8200 (t80) REVERT: B 115 ASP cc_start: 0.7764 (t0) cc_final: 0.7413 (t0) REVERT: D 32 MET cc_start: 0.7607 (tmm) cc_final: 0.7344 (tmm) REVERT: D 117 ASP cc_start: 0.7498 (p0) cc_final: 0.7150 (p0) REVERT: D 129 ASP cc_start: 0.7789 (p0) cc_final: 0.7584 (p0) REVERT: D 164 ASN cc_start: 0.7922 (t0) cc_final: 0.7699 (t0) REVERT: D 165 SER cc_start: 0.8423 (m) cc_final: 0.8139 (p) REVERT: D 172 SER cc_start: 0.8155 (t) cc_final: 0.7917 (p) REVERT: E 58 MET cc_start: 0.7286 (mmt) cc_final: 0.6875 (mmt) REVERT: E 101 MET cc_start: 0.7306 (tpp) cc_final: 0.7009 (tpp) REVERT: F 26 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: F 32 MET cc_start: 0.7169 (tmm) cc_final: 0.6689 (tmm) REVERT: F 117 ASP cc_start: 0.7879 (p0) cc_final: 0.7492 (p0) REVERT: F 131 THR cc_start: 0.8163 (m) cc_final: 0.7682 (p) REVERT: F 158 ASP cc_start: 0.7932 (m-30) cc_final: 0.7642 (m-30) REVERT: F 165 SER cc_start: 0.8502 (m) cc_final: 0.8080 (p) REVERT: G 64 ASP cc_start: 0.7478 (t70) cc_final: 0.7101 (t0) REVERT: I 32 MET cc_start: 0.7187 (tmm) cc_final: 0.6427 (tmm) REVERT: I 37 MET cc_start: 0.8285 (ppp) cc_final: 0.8035 (ptm) REVERT: I 91 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8174 (mp) REVERT: I 101 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.7964 (p) REVERT: I 113 LYS cc_start: 0.6433 (mmtm) cc_final: 0.5375 (ttmm) REVERT: I 165 SER cc_start: 0.8459 (m) cc_final: 0.8119 (p) REVERT: J 8 ASN cc_start: 0.6731 (t0) cc_final: 0.6434 (m-40) REVERT: K 12 TYR cc_start: 0.7035 (m-10) cc_final: 0.6415 (m-10) REVERT: K 32 MET cc_start: 0.7809 (tmm) cc_final: 0.7320 (tmm) REVERT: K 114 TYR cc_start: 0.8240 (t80) cc_final: 0.7885 (t80) REVERT: K 117 ASP cc_start: 0.7336 (p0) cc_final: 0.7135 (p0) REVERT: K 126 SER cc_start: 0.8366 (t) cc_final: 0.8072 (p) REVERT: K 165 SER cc_start: 0.8648 (m) cc_final: 0.8371 (p) outliers start: 79 outliers final: 54 residues processed: 377 average time/residue: 0.2168 time to fit residues: 128.8700 Evaluate side-chains 382 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 0 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 58 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141062 restraints weight = 21365.490| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.64 r_work: 0.3648 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15396 Z= 0.181 Angle : 0.726 12.170 20874 Z= 0.374 Chirality : 0.048 0.171 2346 Planarity : 0.005 0.068 2634 Dihedral : 7.021 51.416 2390 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 5.16 % Allowed : 21.47 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.26 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.15 (0.18), residues: 786 loop : -2.76 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 32 HIS 0.004 0.001 HIS F 96 PHE 0.023 0.002 PHE A 185 TYR 0.017 0.002 TYR D 25 ARG 0.002 0.000 ARG F 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 12) link_NAG-ASN : angle 2.56164 ( 36) hydrogen bonds : bond 0.03994 ( 439) hydrogen bonds : angle 4.91771 ( 1782) SS BOND : bond 0.00545 ( 30) SS BOND : angle 2.33953 ( 60) covalent geometry : bond 0.00408 (15354) covalent geometry : angle 0.70905 (20778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 351 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7447 (tmm) cc_final: 0.7001 (tmm) REVERT: H 25 LEU cc_start: 0.8265 (mt) cc_final: 0.8037 (mm) REVERT: B 12 TYR cc_start: 0.7079 (m-10) cc_final: 0.6648 (m-10) REVERT: B 32 MET cc_start: 0.7588 (tmm) cc_final: 0.6836 (tmm) REVERT: B 91 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 101 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.7916 (p) REVERT: B 114 TYR cc_start: 0.8548 (t80) cc_final: 0.8115 (t80) REVERT: B 115 ASP cc_start: 0.7758 (t0) cc_final: 0.7436 (t0) REVERT: D 32 MET cc_start: 0.7613 (tmm) cc_final: 0.7346 (tmm) REVERT: D 85 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7371 (mt) REVERT: D 117 ASP cc_start: 0.7221 (p0) cc_final: 0.6846 (p0) REVERT: D 129 ASP cc_start: 0.7760 (p0) cc_final: 0.7549 (p0) REVERT: D 163 ARG cc_start: 0.8115 (ptm-80) cc_final: 0.7683 (mtm110) REVERT: D 164 ASN cc_start: 0.7896 (t0) cc_final: 0.7676 (t0) REVERT: D 165 SER cc_start: 0.8437 (m) cc_final: 0.8125 (p) REVERT: D 172 SER cc_start: 0.8136 (t) cc_final: 0.7910 (p) REVERT: E 58 MET cc_start: 0.7275 (mmt) cc_final: 0.6868 (mmt) REVERT: E 101 MET cc_start: 0.7284 (tpp) cc_final: 0.6991 (tpp) REVERT: F 26 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: F 32 MET cc_start: 0.7163 (tmm) cc_final: 0.6749 (tmm) REVERT: F 117 ASP cc_start: 0.7867 (p0) cc_final: 0.7500 (p0) REVERT: F 131 THR cc_start: 0.8147 (m) cc_final: 0.7659 (p) REVERT: F 165 SER cc_start: 0.8477 (m) cc_final: 0.8056 (p) REVERT: G 64 ASP cc_start: 0.7429 (t70) cc_final: 0.7025 (t0) REVERT: G 101 MET cc_start: 0.7581 (tpp) cc_final: 0.7377 (tpp) REVERT: I 32 MET cc_start: 0.7146 (tmm) cc_final: 0.6392 (tmm) REVERT: I 37 MET cc_start: 0.8254 (ppp) cc_final: 0.7980 (ptm) REVERT: I 101 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7983 (p) REVERT: I 113 LYS cc_start: 0.6400 (mmtm) cc_final: 0.5379 (ttmm) REVERT: I 165 SER cc_start: 0.8443 (m) cc_final: 0.8118 (p) REVERT: J 8 ASN cc_start: 0.7001 (t0) cc_final: 0.6738 (m-40) REVERT: K 12 TYR cc_start: 0.6938 (m-10) cc_final: 0.6359 (m-10) REVERT: K 32 MET cc_start: 0.7806 (tmm) cc_final: 0.7322 (tmm) REVERT: K 114 TYR cc_start: 0.8222 (t80) cc_final: 0.7954 (t80) REVERT: K 126 SER cc_start: 0.8389 (t) cc_final: 0.8097 (p) REVERT: K 140 VAL cc_start: 0.7343 (t) cc_final: 0.7101 (p) REVERT: K 165 SER cc_start: 0.8656 (m) cc_final: 0.8346 (p) outliers start: 87 outliers final: 66 residues processed: 403 average time/residue: 0.2115 time to fit residues: 135.6035 Evaluate side-chains 411 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 340 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN B 89 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN I 89 GLN K 97 ASN ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137312 restraints weight = 21504.541| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.76 r_work: 0.3583 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15396 Z= 0.193 Angle : 0.726 11.731 20874 Z= 0.375 Chirality : 0.048 0.185 2346 Planarity : 0.005 0.071 2634 Dihedral : 6.912 55.766 2390 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 6.23 % Allowed : 21.95 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.27 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.20 (0.18), residues: 786 loop : -2.72 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 13 HIS 0.005 0.001 HIS C 99 PHE 0.022 0.002 PHE A 185 TYR 0.016 0.002 TYR D 53 ARG 0.003 0.000 ARG D 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 12) link_NAG-ASN : angle 2.53883 ( 36) hydrogen bonds : bond 0.04007 ( 439) hydrogen bonds : angle 4.94994 ( 1782) SS BOND : bond 0.00561 ( 30) SS BOND : angle 2.43104 ( 60) covalent geometry : bond 0.00439 (15354) covalent geometry : angle 0.70793 (20778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 340 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7574 (tmm) cc_final: 0.7155 (tmm) REVERT: B 12 TYR cc_start: 0.7041 (m-10) cc_final: 0.6630 (m-10) REVERT: B 32 MET cc_start: 0.7590 (tmm) cc_final: 0.6877 (tmm) REVERT: B 91 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 101 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7850 (p) REVERT: B 113 LYS cc_start: 0.6451 (mptt) cc_final: 0.5017 (tttp) REVERT: D 32 MET cc_start: 0.7600 (tmm) cc_final: 0.7345 (tmm) REVERT: D 85 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7258 (mt) REVERT: D 117 ASP cc_start: 0.7267 (p0) cc_final: 0.6873 (p0) REVERT: D 129 ASP cc_start: 0.7719 (p0) cc_final: 0.7493 (p0) REVERT: D 165 SER cc_start: 0.8470 (m) cc_final: 0.8125 (p) REVERT: D 172 SER cc_start: 0.8138 (t) cc_final: 0.7916 (p) REVERT: E 58 MET cc_start: 0.7442 (mmt) cc_final: 0.6999 (mmt) REVERT: E 101 MET cc_start: 0.7366 (tpp) cc_final: 0.7055 (tpp) REVERT: F 26 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: F 32 MET cc_start: 0.7213 (tmm) cc_final: 0.6817 (tmm) REVERT: F 117 ASP cc_start: 0.7877 (p0) cc_final: 0.7530 (p0) REVERT: F 131 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7668 (p) REVERT: F 165 SER cc_start: 0.8453 (m) cc_final: 0.8034 (p) REVERT: G 64 ASP cc_start: 0.7462 (t70) cc_final: 0.6988 (t0) REVERT: G 101 MET cc_start: 0.7638 (tpp) cc_final: 0.7412 (tpp) REVERT: I 32 MET cc_start: 0.7207 (tmm) cc_final: 0.6624 (tmm) REVERT: I 37 MET cc_start: 0.8254 (ppp) cc_final: 0.8025 (ptm) REVERT: I 101 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8018 (p) REVERT: I 113 LYS cc_start: 0.6363 (mmtm) cc_final: 0.5304 (ttmm) REVERT: I 165 SER cc_start: 0.8375 (m) cc_final: 0.8017 (p) REVERT: J 8 ASN cc_start: 0.7215 (t0) cc_final: 0.6966 (m-40) REVERT: K 32 MET cc_start: 0.7849 (tmm) cc_final: 0.7324 (tmm) REVERT: K 126 SER cc_start: 0.8355 (t) cc_final: 0.8038 (p) REVERT: K 131 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7762 (p) REVERT: K 140 VAL cc_start: 0.7385 (t) cc_final: 0.7130 (p) REVERT: K 161 LEU cc_start: 0.8436 (mp) cc_final: 0.8196 (mp) REVERT: K 165 SER cc_start: 0.8662 (m) cc_final: 0.8356 (p) outliers start: 105 outliers final: 82 residues processed: 399 average time/residue: 0.2057 time to fit residues: 129.9102 Evaluate side-chains 423 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 334 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 97 ASN I 108 ASN ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.162540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138278 restraints weight = 21464.563| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.76 r_work: 0.3593 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15396 Z= 0.176 Angle : 0.708 10.705 20874 Z= 0.365 Chirality : 0.047 0.184 2346 Planarity : 0.005 0.067 2634 Dihedral : 6.627 57.068 2390 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 5.99 % Allowed : 23.13 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 2.08 % 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: -2.22 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.22 (0.18), residues: 798 loop : -2.67 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 13 HIS 0.004 0.001 HIS L 99 PHE 0.021 0.002 PHE A 185 TYR 0.016 0.001 TYR K 25 ARG 0.002 0.000 ARG F 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 12) link_NAG-ASN : angle 2.47210 ( 36) hydrogen bonds : bond 0.03826 ( 439) hydrogen bonds : angle 4.84820 ( 1782) SS BOND : bond 0.00523 ( 30) SS BOND : angle 2.24829 ( 60) covalent geometry : bond 0.00395 (15354) covalent geometry : angle 0.69211 (20778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 337 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.7518 (tmm) cc_final: 0.7124 (tmm) REVERT: B 32 MET cc_start: 0.7552 (tmm) cc_final: 0.6846 (tmm) REVERT: B 101 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7813 (p) REVERT: B 113 LYS cc_start: 0.6409 (mptt) cc_final: 0.4996 (tttp) REVERT: D 32 MET cc_start: 0.7635 (tmm) cc_final: 0.7398 (tmm) REVERT: D 85 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7214 (mt) REVERT: D 117 ASP cc_start: 0.7320 (p0) cc_final: 0.6941 (p0) REVERT: D 129 ASP cc_start: 0.7698 (p0) cc_final: 0.7474 (p0) REVERT: D 165 SER cc_start: 0.8469 (m) cc_final: 0.8145 (p) REVERT: D 172 SER cc_start: 0.8216 (t) cc_final: 0.7959 (p) REVERT: E 58 MET cc_start: 0.7419 (mmt) cc_final: 0.6978 (mmt) REVERT: E 101 MET cc_start: 0.7338 (tpp) cc_final: 0.7034 (tpp) REVERT: F 26 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: F 32 MET cc_start: 0.7294 (tmm) cc_final: 0.6968 (tmm) REVERT: F 117 ASP cc_start: 0.7864 (p0) cc_final: 0.7527 (p0) REVERT: F 131 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7669 (p) REVERT: F 165 SER cc_start: 0.8452 (m) cc_final: 0.8020 (p) REVERT: G 64 ASP cc_start: 0.7517 (t70) cc_final: 0.6932 (t70) REVERT: I 32 MET cc_start: 0.7202 (tmm) cc_final: 0.6615 (tmm) REVERT: I 91 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8321 (mp) REVERT: I 101 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8001 (p) REVERT: I 113 LYS cc_start: 0.6319 (mmtm) cc_final: 0.5264 (ttmm) REVERT: I 165 SER cc_start: 0.8447 (m) cc_final: 0.8073 (p) REVERT: K 12 TYR cc_start: 0.7039 (m-10) cc_final: 0.6435 (m-10) REVERT: K 32 MET cc_start: 0.7864 (tmm) cc_final: 0.7322 (tmm) REVERT: K 126 SER cc_start: 0.8363 (t) cc_final: 0.8056 (p) REVERT: K 140 VAL cc_start: 0.7379 (t) cc_final: 0.7130 (p) REVERT: K 161 LEU cc_start: 0.8538 (mp) cc_final: 0.8281 (mp) REVERT: K 165 SER cc_start: 0.8663 (m) cc_final: 0.8361 (p) outliers start: 101 outliers final: 85 residues processed: 394 average time/residue: 0.2072 time to fit residues: 129.5945 Evaluate side-chains 426 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 335 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 111 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 155 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN D 155 HIS I 79 ASN ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139323 restraints weight = 21484.794| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.78 r_work: 0.3611 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15396 Z= 0.149 Angle : 0.696 9.458 20874 Z= 0.355 Chirality : 0.047 0.162 2346 Planarity : 0.005 0.064 2634 Dihedral : 6.379 59.536 2390 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 5.75 % Allowed : 24.26 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.23 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.24 (0.18), residues: 798 loop : -2.66 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 32 HIS 0.003 0.001 HIS C 99 PHE 0.019 0.001 PHE A 185 TYR 0.015 0.001 TYR K 25 ARG 0.002 0.000 ARG D 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 12) link_NAG-ASN : angle 2.34181 ( 36) hydrogen bonds : bond 0.03651 ( 439) hydrogen bonds : angle 4.72314 ( 1782) SS BOND : bond 0.00470 ( 30) SS BOND : angle 2.07147 ( 60) covalent geometry : bond 0.00331 (15354) covalent geometry : angle 0.68129 (20778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 331 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7614 (m-30) cc_final: 0.7405 (m-30) REVERT: A 32 MET cc_start: 0.7534 (tmm) cc_final: 0.7148 (tmm) REVERT: B 32 MET cc_start: 0.7522 (tmm) cc_final: 0.6833 (tmm) REVERT: B 101 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7745 (p) REVERT: B 113 LYS cc_start: 0.6400 (mptt) cc_final: 0.4909 (tttm) REVERT: B 172 SER cc_start: 0.8365 (p) cc_final: 0.8157 (p) REVERT: D 32 MET cc_start: 0.7657 (tmm) cc_final: 0.7422 (tmm) REVERT: D 85 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7299 (mt) REVERT: D 117 ASP cc_start: 0.7315 (p0) cc_final: 0.6936 (p0) REVERT: D 129 ASP cc_start: 0.7641 (p0) cc_final: 0.7414 (p0) REVERT: D 163 ARG cc_start: 0.8194 (ptm-80) cc_final: 0.7806 (mtm110) REVERT: D 165 SER cc_start: 0.8484 (m) cc_final: 0.8140 (p) REVERT: D 172 SER cc_start: 0.8206 (t) cc_final: 0.7946 (p) REVERT: E 58 MET cc_start: 0.7466 (mmt) cc_final: 0.6908 (mmt) REVERT: E 101 MET cc_start: 0.7353 (tpp) cc_final: 0.7032 (tpp) REVERT: F 11 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6284 (mpt180) REVERT: F 26 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: F 32 MET cc_start: 0.7313 (tmm) cc_final: 0.7025 (tmm) REVERT: F 117 ASP cc_start: 0.7833 (p0) cc_final: 0.7502 (p0) REVERT: F 165 SER cc_start: 0.8446 (m) cc_final: 0.8027 (p) REVERT: G 64 ASP cc_start: 0.7508 (t70) cc_final: 0.6958 (t70) REVERT: I 32 MET cc_start: 0.7199 (tmm) cc_final: 0.6631 (tmm) REVERT: I 101 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.7952 (p) REVERT: I 113 LYS cc_start: 0.6305 (mmtm) cc_final: 0.5336 (tttp) REVERT: I 165 SER cc_start: 0.8438 (m) cc_final: 0.8052 (p) REVERT: K 12 TYR cc_start: 0.6978 (m-10) cc_final: 0.6372 (m-10) REVERT: K 32 MET cc_start: 0.7817 (tmm) cc_final: 0.7281 (tmm) REVERT: K 126 SER cc_start: 0.8360 (t) cc_final: 0.8033 (p) REVERT: K 140 VAL cc_start: 0.7360 (t) cc_final: 0.7096 (p) REVERT: K 161 LEU cc_start: 0.8549 (mp) cc_final: 0.8302 (mp) REVERT: K 165 SER cc_start: 0.8651 (m) cc_final: 0.8345 (p) outliers start: 97 outliers final: 75 residues processed: 388 average time/residue: 0.2017 time to fit residues: 124.5697 Evaluate side-chains 405 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 325 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 165 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 155 HIS B 89 GLN G 88 HIS G 102 ASN I 79 ASN ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140555 restraints weight = 21357.004| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.76 r_work: 0.3624 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15396 Z= 0.133 Angle : 0.675 9.327 20874 Z= 0.343 Chirality : 0.046 0.162 2346 Planarity : 0.004 0.059 2634 Dihedral : 6.081 57.892 2390 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 5.10 % Allowed : 24.67 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.23 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.23 (0.18), residues: 798 loop : -2.67 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 32 HIS 0.003 0.001 HIS L 99 PHE 0.017 0.001 PHE A 185 TYR 0.014 0.001 TYR K 25 ARG 0.002 0.000 ARG F 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 12) link_NAG-ASN : angle 2.16065 ( 36) hydrogen bonds : bond 0.03521 ( 439) hydrogen bonds : angle 4.61447 ( 1782) SS BOND : bond 0.00447 ( 30) SS BOND : angle 1.95757 ( 60) covalent geometry : bond 0.00292 (15354) covalent geometry : angle 0.66196 (20778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 328 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7564 (m-30) cc_final: 0.7345 (m-30) REVERT: A 32 MET cc_start: 0.7543 (tmm) cc_final: 0.7176 (tmm) REVERT: B 32 MET cc_start: 0.7464 (tmm) cc_final: 0.6794 (tmm) REVERT: B 101 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7717 (p) REVERT: B 113 LYS cc_start: 0.6424 (mptt) cc_final: 0.4954 (tttm) REVERT: D 32 MET cc_start: 0.7626 (tmm) cc_final: 0.7417 (tmm) REVERT: D 85 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7296 (mt) REVERT: D 117 ASP cc_start: 0.7284 (p0) cc_final: 0.6917 (p0) REVERT: D 129 ASP cc_start: 0.7597 (p0) cc_final: 0.7367 (p0) REVERT: D 165 SER cc_start: 0.8478 (m) cc_final: 0.8147 (p) REVERT: D 172 SER cc_start: 0.8194 (t) cc_final: 0.7972 (p) REVERT: E 58 MET cc_start: 0.7439 (mmt) cc_final: 0.6889 (mmt) REVERT: E 101 MET cc_start: 0.7337 (tpp) cc_final: 0.7009 (tpp) REVERT: F 11 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6081 (mpt180) REVERT: F 32 MET cc_start: 0.7330 (tmm) cc_final: 0.7065 (tmm) REVERT: F 117 ASP cc_start: 0.7773 (p0) cc_final: 0.7468 (p0) REVERT: F 165 SER cc_start: 0.8473 (m) cc_final: 0.8032 (p) REVERT: G 64 ASP cc_start: 0.7487 (t70) cc_final: 0.6893 (t70) REVERT: I 32 MET cc_start: 0.7128 (tmm) cc_final: 0.6567 (tmm) REVERT: I 91 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8337 (mp) REVERT: I 101 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.7963 (p) REVERT: I 113 LYS cc_start: 0.6288 (mmtm) cc_final: 0.5376 (tttp) REVERT: I 165 SER cc_start: 0.8450 (m) cc_final: 0.8051 (p) REVERT: K 12 TYR cc_start: 0.6986 (m-10) cc_final: 0.6349 (m-10) REVERT: K 32 MET cc_start: 0.7759 (tmm) cc_final: 0.7234 (tmm) REVERT: K 114 TYR cc_start: 0.8222 (t80) cc_final: 0.7948 (t80) REVERT: K 126 SER cc_start: 0.8358 (t) cc_final: 0.8011 (p) REVERT: K 140 VAL cc_start: 0.7345 (t) cc_final: 0.7092 (p) REVERT: K 161 LEU cc_start: 0.8523 (mp) cc_final: 0.8283 (mp) REVERT: K 165 SER cc_start: 0.8655 (m) cc_final: 0.8356 (p) REVERT: L 4 GLN cc_start: 0.6892 (tp40) cc_final: 0.6659 (tp40) outliers start: 86 outliers final: 68 residues processed: 376 average time/residue: 0.2055 time to fit residues: 123.4383 Evaluate side-chains 399 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 326 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 165 optimal weight: 0.0570 chunk 116 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 0.0070 chunk 122 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN H 102 ASN D 79 ASN G 89 HIS I 79 ASN ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.167604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143289 restraints weight = 21268.648| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.79 r_work: 0.3667 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15396 Z= 0.112 Angle : 0.658 10.331 20874 Z= 0.333 Chirality : 0.045 0.218 2346 Planarity : 0.004 0.053 2634 Dihedral : 5.746 53.479 2390 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 4.15 % Allowed : 25.80 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 2.08 % 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: -2.17 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.23 (0.19), residues: 762 loop : -2.52 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 13 HIS 0.003 0.000 HIS C 99 PHE 0.018 0.001 PHE F 185 TYR 0.015 0.001 TYR K 25 ARG 0.002 0.000 ARG F 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 12) link_NAG-ASN : angle 1.95992 ( 36) hydrogen bonds : bond 0.03291 ( 439) hydrogen bonds : angle 4.47849 ( 1782) SS BOND : bond 0.00353 ( 30) SS BOND : angle 1.92210 ( 60) covalent geometry : bond 0.00238 (15354) covalent geometry : angle 0.64611 (20778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 326 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7533 (m-30) cc_final: 0.7293 (m-30) REVERT: A 32 MET cc_start: 0.7566 (tmm) cc_final: 0.7245 (tmm) REVERT: B 11 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5893 (mpt180) REVERT: B 32 MET cc_start: 0.7473 (tmm) cc_final: 0.6794 (tmm) REVERT: B 101 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7670 (p) REVERT: B 113 LYS cc_start: 0.6485 (mptt) cc_final: 0.5074 (tttm) REVERT: B 115 ASP cc_start: 0.7652 (t0) cc_final: 0.7449 (t0) REVERT: D 85 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7222 (mt) REVERT: D 117 ASP cc_start: 0.7275 (p0) cc_final: 0.6906 (p0) REVERT: D 158 ASP cc_start: 0.7711 (m-30) cc_final: 0.7461 (m-30) REVERT: D 165 SER cc_start: 0.8492 (m) cc_final: 0.8142 (p) REVERT: E 58 MET cc_start: 0.7414 (mmt) cc_final: 0.6851 (mmt) REVERT: E 101 MET cc_start: 0.7369 (tpp) cc_final: 0.7019 (tpp) REVERT: F 11 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5963 (mpt180) REVERT: F 26 ASP cc_start: 0.7519 (m-30) cc_final: 0.7153 (m-30) REVERT: F 32 MET cc_start: 0.7346 (tmm) cc_final: 0.6982 (tmm) REVERT: F 165 SER cc_start: 0.8468 (m) cc_final: 0.8034 (p) REVERT: G 64 ASP cc_start: 0.7543 (t70) cc_final: 0.6950 (t70) REVERT: I 32 MET cc_start: 0.7123 (tmm) cc_final: 0.6575 (tmm) REVERT: I 91 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8220 (mp) REVERT: I 92 ASP cc_start: 0.7350 (t0) cc_final: 0.7148 (m-30) REVERT: I 101 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7897 (p) REVERT: I 113 LYS cc_start: 0.6117 (mmtm) cc_final: 0.5225 (tttp) REVERT: K 32 MET cc_start: 0.7759 (tmm) cc_final: 0.7233 (tmm) REVERT: K 140 VAL cc_start: 0.7322 (t) cc_final: 0.7096 (p) REVERT: K 161 LEU cc_start: 0.8487 (mp) cc_final: 0.8267 (mp) REVERT: K 165 SER cc_start: 0.8630 (m) cc_final: 0.8337 (p) REVERT: L 4 GLN cc_start: 0.6952 (tp40) cc_final: 0.6711 (tp40) outliers start: 70 outliers final: 53 residues processed: 369 average time/residue: 0.2139 time to fit residues: 123.6374 Evaluate side-chains 380 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 321 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 143 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN I 79 ASN I 89 GLN ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.160272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136209 restraints weight = 21438.824| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.73 r_work: 0.3568 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15396 Z= 0.250 Angle : 0.797 11.413 20874 Z= 0.410 Chirality : 0.050 0.236 2346 Planarity : 0.005 0.067 2634 Dihedral : 6.577 47.633 2384 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.80 % Allowed : 26.63 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.19 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.15 (0.18), residues: 798 loop : -2.71 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 13 HIS 0.006 0.001 HIS K 96 PHE 0.028 0.002 PHE F 185 TYR 0.023 0.002 TYR F 25 ARG 0.008 0.001 ARG H 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 12) link_NAG-ASN : angle 2.41845 ( 36) hydrogen bonds : bond 0.04209 ( 439) hydrogen bonds : angle 4.88694 ( 1782) SS BOND : bond 0.00615 ( 30) SS BOND : angle 2.63253 ( 60) covalent geometry : bond 0.00573 (15354) covalent geometry : angle 0.78011 (20778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6030 (mpt180) REVERT: A 32 MET cc_start: 0.7547 (tmm) cc_final: 0.7196 (tmm) REVERT: A 117 ASP cc_start: 0.7689 (p0) cc_final: 0.7489 (p0) REVERT: A 126 SER cc_start: 0.8235 (t) cc_final: 0.7881 (p) REVERT: B 11 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6445 (mpt180) REVERT: B 32 MET cc_start: 0.7521 (tmm) cc_final: 0.6841 (tmm) REVERT: B 101 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 113 LYS cc_start: 0.6559 (mptt) cc_final: 0.5121 (tttm) REVERT: D 11 ARG cc_start: 0.6925 (mpp-170) cc_final: 0.6649 (mpt180) REVERT: D 32 MET cc_start: 0.7745 (tmm) cc_final: 0.7293 (tmm) REVERT: D 85 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7245 (mt) REVERT: D 117 ASP cc_start: 0.7441 (p0) cc_final: 0.7086 (p0) REVERT: D 165 SER cc_start: 0.8464 (m) cc_final: 0.8091 (p) REVERT: E 58 MET cc_start: 0.7445 (mmt) cc_final: 0.6948 (mmt) REVERT: E 101 MET cc_start: 0.7304 (tpp) cc_final: 0.7001 (tpp) REVERT: F 26 ASP cc_start: 0.7642 (m-30) cc_final: 0.7360 (m-30) REVERT: F 32 MET cc_start: 0.7387 (tmm) cc_final: 0.7004 (tmm) REVERT: F 117 ASP cc_start: 0.7832 (p0) cc_final: 0.7489 (p0) REVERT: F 165 SER cc_start: 0.8506 (m) cc_final: 0.8037 (p) REVERT: G 64 ASP cc_start: 0.7655 (t70) cc_final: 0.7039 (t70) REVERT: I 32 MET cc_start: 0.7229 (tmm) cc_final: 0.6706 (tmm) REVERT: I 91 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8102 (mp) REVERT: I 92 ASP cc_start: 0.7364 (t0) cc_final: 0.7054 (m-30) REVERT: I 101 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7969 (p) REVERT: I 113 LYS cc_start: 0.6072 (mmtm) cc_final: 0.5274 (ttmm) REVERT: K 32 MET cc_start: 0.7887 (tmm) cc_final: 0.7366 (tmm) REVERT: K 73 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7339 (mt-10) REVERT: K 114 TYR cc_start: 0.8205 (t80) cc_final: 0.7901 (t80) REVERT: K 126 SER cc_start: 0.8392 (t) cc_final: 0.8071 (p) REVERT: K 140 VAL cc_start: 0.7368 (t) cc_final: 0.7126 (p) REVERT: K 165 SER cc_start: 0.8661 (m) cc_final: 0.8368 (p) outliers start: 64 outliers final: 53 residues processed: 361 average time/residue: 0.2125 time to fit residues: 120.3555 Evaluate side-chains 379 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 320 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 4 CYS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 35 CYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 35 CYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 0.1980 chunk 81 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 89 GLN D 108 ASN I 89 GLN ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140046 restraints weight = 21391.385| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.77 r_work: 0.3620 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15396 Z= 0.140 Angle : 0.713 11.060 20874 Z= 0.363 Chirality : 0.046 0.226 2346 Planarity : 0.005 0.060 2634 Dihedral : 5.961 48.667 2384 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.74 % Allowed : 26.45 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: -2.21 (0.19), residues: 1812 helix: None (None), residues: 0 sheet: -0.22 (0.18), residues: 798 loop : -2.66 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 13 HIS 0.003 0.001 HIS A 152 PHE 0.023 0.001 PHE F 185 TYR 0.017 0.001 TYR K 162 ARG 0.004 0.000 ARG H 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 12) link_NAG-ASN : angle 2.17416 ( 36) hydrogen bonds : bond 0.03551 ( 439) hydrogen bonds : angle 4.66068 ( 1782) SS BOND : bond 0.00386 ( 30) SS BOND : angle 2.11908 ( 60) covalent geometry : bond 0.00309 (15354) covalent geometry : angle 0.69962 (20778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6209.93 seconds wall clock time: 108 minutes 56.68 seconds (6536.68 seconds total)