Starting phenix.real_space_refine on Sat Aug 23 16:40:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce4_16598/08_2025/8ce4_16598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce4_16598/08_2025/8ce4_16598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ce4_16598/08_2025/8ce4_16598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce4_16598/08_2025/8ce4_16598.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce4_16598/08_2025/8ce4_16598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce4_16598/08_2025/8ce4_16598.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 70 5.16 5 C 8515 2.51 5 N 2280 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13435 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "B" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "C" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "E" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "F" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.63, per 1000 atoms: 0.34 Number of scatterers: 13435 At special positions: 0 Unit cell: (90.644, 92.106, 113.305, 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 70 16.00 O 2570 8.00 N 2280 7.00 C 8515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 95 " - pdb=" SG CYS F 114 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 95 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 95 " - pdb=" SG CYS H 114 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 95 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 95 " - pdb=" SG CYS J 114 " 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 BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 657.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 30 sheets defined 8.2% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.662A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.758A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.742A pdb=" N GLU F 110 " --> pdb=" O ALA F 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.663A pdb=" N GLU H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 107 through 111 removed outlier: 3.588A pdb=" N GLU I 110 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.051A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.051A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.980A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.980A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.545A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.143A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.143A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 48 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL C 42 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 50 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 38 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP C 54 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU C 36 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN C 56 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU C 34 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE C 32 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL C 30 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.528A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.854A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.854A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.533A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.555A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.553A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.562A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.581A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.631A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.530A pdb=" N GLY J 10 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1230 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: 2.58 Time building geometry restraints manager: 1.24 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: 4318 1.35 - 1.47: 3743 1.47 - 1.59: 5648 1.59 - 1.71: 1 1.71 - 1.83: 95 Bond restraints: 13805 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CB PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.24e+00 ... (remaining 13800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 18328 1.88 - 3.77: 366 3.77 - 5.65: 54 5.65 - 7.53: 5 7.53 - 9.42: 2 Bond angle restraints: 18755 Sorted by residual: angle pdb=" CA PRO F 88 " pdb=" N PRO F 88 " pdb=" CD PRO F 88 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.52e+01 angle pdb=" CA PRO D 169 " pdb=" N PRO D 169 " pdb=" CD PRO D 169 " ideal model delta sigma weight residual 112.00 104.69 7.31 1.40e+00 5.10e-01 2.73e+01 angle pdb=" C TRP E 133 " pdb=" N PHE E 134 " pdb=" CA PHE E 134 " ideal model delta sigma weight residual 121.80 130.64 -8.84 2.44e+00 1.68e-01 1.31e+01 angle pdb=" N PRO F 88 " pdb=" CD PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 103.20 98.02 5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 112.00 107.83 4.17 1.40e+00 5.10e-01 8.87e+00 ... (remaining 18750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 7563 25.07 - 50.15: 656 50.15 - 75.22: 137 75.22 - 100.29: 14 100.29 - 125.36: 8 Dihedral angle restraints: 8378 sinusoidal: 3603 harmonic: 4775 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " pdb=" SG CYS H 114 " pdb=" CB CYS H 114 " ideal model delta sinusoidal sigma weight residual 93.00 35.04 57.96 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS I 95 " pdb=" SG CYS I 95 " pdb=" SG CYS I 114 " pdb=" CB CYS I 114 " ideal model delta sinusoidal sigma weight residual 93.00 37.20 55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 8375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1541 0.044 - 0.087: 344 0.087 - 0.131: 113 0.131 - 0.175: 9 0.175 - 0.218: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 178 " pdb=" CA ILE A 178 " pdb=" CG1 ILE A 178 " pdb=" CG2 ILE A 178 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CB ILE E 178 " pdb=" CA ILE E 178 " pdb=" CG1 ILE E 178 " pdb=" CG2 ILE E 178 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2007 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 168 " -0.096 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO D 169 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 87 " -0.069 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO F 88 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 168 " 0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO B 169 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " 0.050 5.00e-02 4.00e+02 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 474 2.71 - 3.26: 12004 3.26 - 3.80: 22376 3.80 - 4.35: 30099 4.35 - 4.90: 49427 Nonbonded interactions: 114380 Sorted by model distance: nonbonded pdb=" O TYR I 32 " pdb=" NH2 ARG I 72 " model vdw 2.159 3.120 nonbonded pdb=" O TYR G 32 " pdb=" NH2 ARG G 72 " model vdw 2.170 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 72 " model vdw 2.174 3.120 nonbonded pdb=" O TYR F 32 " pdb=" NH2 ARG F 72 " model vdw 2.175 3.120 nonbonded pdb=" O TYR J 32 " pdb=" NH2 ARG J 72 " model vdw 2.186 3.120 ... (remaining 114375 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 402)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 402)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 402)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 402)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.40 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.060 Find NCS groups from input model: 0.280 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 32.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 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 : 0.004 0.135 13841 Z= 0.174 Angle : 0.649 11.167 18847 Z= 0.334 Chirality : 0.043 0.218 2010 Planarity : 0.007 0.140 2410 Dihedral : 18.891 125.364 5280 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 2.61 % Allowed : 26.69 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.19), residues: 1630 helix: 3.20 (0.66), residues: 45 sheet: -0.35 (0.19), residues: 660 loop : -0.87 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 204 TYR 0.019 0.001 TYR E 128 PHE 0.020 0.001 PHE A 136 TRP 0.013 0.001 TRP A 153 HIS 0.002 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00424 (13805) covalent geometry : angle 0.62555 (18755) SS BOND : bond 0.00437 ( 16) SS BOND : angle 0.76058 ( 32) hydrogen bonds : bond 0.13933 ( 421) hydrogen bonds : angle 6.67362 ( 1230) link_BETA1-4 : bond 0.01127 ( 5) link_BETA1-4 : angle 5.20246 ( 15) link_NAG-ASN : bond 0.00164 ( 15) link_NAG-ASN : angle 2.03378 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8524 (tmtt) REVERT: I 45 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7422 (ttm-80) REVERT: J 45 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7398 (tpp80) outliers start: 37 outliers final: 27 residues processed: 321 average time/residue: 0.7254 time to fit residues: 247.3589 Evaluate side-chains 280 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 56 GLN B 3 GLN B 46 ASN C 26 GLN C 46 ASN C 116 GLN D 46 ASN E 46 ASN F 13 GLN G 13 GLN H 13 GLN I 13 GLN I 84 ASN J 5 GLN J 13 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.073047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.052771 restraints weight = 33228.519| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 2.97 r_work: 0.2412 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2287 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2283 r_free = 0.2283 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2283 r_free = 0.2283 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13841 Z= 0.274 Angle : 0.704 8.680 18847 Z= 0.355 Chirality : 0.045 0.295 2010 Planarity : 0.007 0.101 2410 Dihedral : 12.031 114.152 2269 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 4.65 % Allowed : 24.08 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.19), residues: 1630 helix: 1.83 (0.73), residues: 50 sheet: -0.30 (0.19), residues: 655 loop : -0.90 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 72 TYR 0.016 0.002 TYR A 117 PHE 0.017 0.002 PHE C 2 TRP 0.020 0.002 TRP B 133 HIS 0.004 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00630 (13805) covalent geometry : angle 0.67930 (18755) SS BOND : bond 0.00462 ( 16) SS BOND : angle 0.94780 ( 32) hydrogen bonds : bond 0.03971 ( 421) hydrogen bonds : angle 5.64292 ( 1230) link_BETA1-4 : bond 0.00959 ( 5) link_BETA1-4 : angle 5.25695 ( 15) link_NAG-ASN : bond 0.00436 ( 15) link_NAG-ASN : angle 2.30019 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 0.401 Fit side-chains REVERT: A 191 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8143 (tmtt) REVERT: G 13 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7272 (mm110) REVERT: H 73 ASP cc_start: 0.9115 (t0) cc_final: 0.8817 (t0) REVERT: I 13 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7229 (mm110) REVERT: I 73 ASP cc_start: 0.9059 (t0) cc_final: 0.8789 (t0) REVERT: J 13 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7093 (mm110) REVERT: J 84 ASN cc_start: 0.8264 (m-40) cc_final: 0.7898 (m-40) outliers start: 66 outliers final: 28 residues processed: 311 average time/residue: 0.7276 time to fit residues: 240.4943 Evaluate side-chains 282 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 140 optimal weight: 0.0970 chunk 115 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN C 26 GLN C 116 GLN D 46 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 13 GLN H 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.053403 restraints weight = 63843.884| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 3.89 r_work: 0.2411 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2408 r_free = 0.2408 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13841 Z= 0.146 Angle : 0.635 8.392 18847 Z= 0.320 Chirality : 0.042 0.247 2010 Planarity : 0.005 0.085 2410 Dihedral : 11.357 115.876 2255 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.31 % Allowed : 25.07 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.19), residues: 1630 helix: 2.94 (0.72), residues: 45 sheet: -0.26 (0.19), residues: 650 loop : -1.05 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 204 TYR 0.015 0.001 TYR B 117 PHE 0.015 0.001 PHE E 136 TRP 0.029 0.001 TRP B 133 HIS 0.002 0.000 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00339 (13805) covalent geometry : angle 0.60914 (18755) SS BOND : bond 0.00316 ( 16) SS BOND : angle 0.72801 ( 32) hydrogen bonds : bond 0.03125 ( 421) hydrogen bonds : angle 5.33475 ( 1230) link_BETA1-4 : bond 0.01225 ( 5) link_BETA1-4 : angle 5.02928 ( 15) link_NAG-ASN : bond 0.00198 ( 15) link_NAG-ASN : angle 2.29613 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 0.564 Fit side-chains REVERT: A 75 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9179 (mtmm) REVERT: A 191 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8182 (tmtt) REVERT: A 205 ARG cc_start: 0.8232 (ttp-170) cc_final: 0.7879 (ttp-170) REVERT: B 97 GLU cc_start: 0.9064 (pt0) cc_final: 0.8773 (mp0) REVERT: B 130 ASP cc_start: 0.8057 (t0) cc_final: 0.7856 (t0) REVERT: C 172 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8780 (tt0) REVERT: D 97 GLU cc_start: 0.9164 (pt0) cc_final: 0.8777 (mp0) REVERT: D 192 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: E 97 GLU cc_start: 0.9074 (pt0) cc_final: 0.8716 (mp0) REVERT: F 13 GLN cc_start: 0.7541 (mm-40) cc_final: 0.6916 (mm110) REVERT: H 13 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7022 (mm110) REVERT: H 73 ASP cc_start: 0.9058 (t0) cc_final: 0.8712 (t0) REVERT: I 45 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8270 (ttp80) REVERT: I 73 ASP cc_start: 0.9002 (t0) cc_final: 0.8693 (t0) REVERT: J 108 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8290 (mtt180) outliers start: 47 outliers final: 23 residues processed: 296 average time/residue: 0.7420 time to fit residues: 232.8010 Evaluate side-chains 283 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN G 13 GLN J 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.052772 restraints weight = 58582.079| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.74 r_work: 0.2398 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2394 r_free = 0.2394 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2394 r_free = 0.2394 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13841 Z= 0.177 Angle : 0.640 8.095 18847 Z= 0.321 Chirality : 0.042 0.224 2010 Planarity : 0.005 0.077 2410 Dihedral : 10.876 115.288 2246 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.08 % Allowed : 24.23 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.19), residues: 1630 helix: 1.99 (0.76), residues: 50 sheet: -0.25 (0.19), residues: 650 loop : -1.09 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 204 TYR 0.012 0.001 TYR B 117 PHE 0.013 0.001 PHE C 2 TRP 0.029 0.001 TRP D 133 HIS 0.003 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00406 (13805) covalent geometry : angle 0.61405 (18755) SS BOND : bond 0.00348 ( 16) SS BOND : angle 0.81452 ( 32) hydrogen bonds : bond 0.03125 ( 421) hydrogen bonds : angle 5.24231 ( 1230) link_BETA1-4 : bond 0.01100 ( 5) link_BETA1-4 : angle 5.01153 ( 15) link_NAG-ASN : bond 0.00283 ( 15) link_NAG-ASN : angle 2.32382 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 257 time to evaluate : 0.455 Fit side-chains REVERT: A 75 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9198 (mtmm) REVERT: A 97 GLU cc_start: 0.9057 (pt0) cc_final: 0.8729 (mp0) REVERT: A 191 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8189 (tmtt) REVERT: B 97 GLU cc_start: 0.9071 (pt0) cc_final: 0.8767 (mp0) REVERT: B 192 GLU cc_start: 0.8455 (tp30) cc_final: 0.8219 (tp30) REVERT: C 1 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: C 192 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8087 (tp30) REVERT: D 97 GLU cc_start: 0.9150 (pt0) cc_final: 0.8770 (mp0) REVERT: D 192 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8158 (tp30) REVERT: E 97 GLU cc_start: 0.9062 (pt0) cc_final: 0.8733 (mp0) REVERT: F 43 LYS cc_start: 0.9271 (ttmm) cc_final: 0.9040 (mppt) REVERT: H 73 ASP cc_start: 0.9083 (t0) cc_final: 0.8730 (t0) REVERT: I 73 ASP cc_start: 0.9040 (t0) cc_final: 0.8670 (t0) REVERT: J 108 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8236 (mtt180) outliers start: 58 outliers final: 23 residues processed: 298 average time/residue: 0.7669 time to fit residues: 242.6187 Evaluate side-chains 276 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 13 GLN G 13 GLN H 13 GLN I 13 GLN J 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.053627 restraints weight = 57122.703| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 3.75 r_work: 0.2427 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13841 Z= 0.142 Angle : 0.627 8.077 18847 Z= 0.315 Chirality : 0.041 0.205 2010 Planarity : 0.005 0.072 2410 Dihedral : 10.531 115.174 2245 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.17 % Allowed : 25.77 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.19), residues: 1630 helix: 2.05 (0.77), residues: 50 sheet: -0.20 (0.19), residues: 650 loop : -1.14 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.011 0.001 TYR C 117 PHE 0.010 0.001 PHE C 2 TRP 0.051 0.002 TRP E 133 HIS 0.002 0.000 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00329 (13805) covalent geometry : angle 0.60314 (18755) SS BOND : bond 0.00294 ( 16) SS BOND : angle 0.72421 ( 32) hydrogen bonds : bond 0.02824 ( 421) hydrogen bonds : angle 5.08984 ( 1230) link_BETA1-4 : bond 0.01280 ( 5) link_BETA1-4 : angle 4.83081 ( 15) link_NAG-ASN : bond 0.00196 ( 15) link_NAG-ASN : angle 2.22756 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.521 Fit side-chains REVERT: A 75 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9160 (mtmm) REVERT: A 97 GLU cc_start: 0.9067 (pt0) cc_final: 0.8724 (mp0) REVERT: A 172 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8784 (tt0) REVERT: A 191 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8192 (tmtt) REVERT: C 181 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9175 (ptmm) REVERT: C 192 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8077 (tp30) REVERT: D 43 ASP cc_start: 0.9287 (t0) cc_final: 0.8955 (t0) REVERT: D 97 GLU cc_start: 0.9144 (pt0) cc_final: 0.8720 (mp0) REVERT: D 192 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: E 97 GLU cc_start: 0.9068 (pt0) cc_final: 0.8722 (mp0) REVERT: F 43 LYS cc_start: 0.9287 (ttmm) cc_final: 0.9063 (mppt) REVERT: H 73 ASP cc_start: 0.9079 (t0) cc_final: 0.8694 (t0) REVERT: I 45 ARG cc_start: 0.8419 (ttp80) cc_final: 0.7911 (tpp80) REVERT: I 73 ASP cc_start: 0.9018 (t0) cc_final: 0.8692 (t0) outliers start: 45 outliers final: 17 residues processed: 294 average time/residue: 0.7915 time to fit residues: 247.0152 Evaluate side-chains 266 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 124 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN G 13 GLN I 13 GLN J 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.052869 restraints weight = 58760.553| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 3.77 r_work: 0.2404 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13841 Z= 0.170 Angle : 0.643 7.841 18847 Z= 0.323 Chirality : 0.042 0.202 2010 Planarity : 0.005 0.068 2410 Dihedral : 10.392 115.327 2243 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.61 % Allowed : 26.13 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.19), residues: 1630 helix: 1.90 (0.77), residues: 50 sheet: -0.22 (0.19), residues: 650 loop : -1.16 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 204 TYR 0.012 0.001 TYR D 128 PHE 0.011 0.001 PHE C 2 TRP 0.050 0.002 TRP E 133 HIS 0.002 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00393 (13805) covalent geometry : angle 0.61959 (18755) SS BOND : bond 0.00339 ( 16) SS BOND : angle 0.83134 ( 32) hydrogen bonds : bond 0.02952 ( 421) hydrogen bonds : angle 5.11877 ( 1230) link_BETA1-4 : bond 0.01112 ( 5) link_BETA1-4 : angle 4.82092 ( 15) link_NAG-ASN : bond 0.00261 ( 15) link_NAG-ASN : angle 2.21532 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.359 Fit side-chains REVERT: A 75 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9199 (mtmm) REVERT: A 97 GLU cc_start: 0.9083 (pt0) cc_final: 0.8698 (mp0) REVERT: A 172 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8782 (tt0) REVERT: A 191 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8177 (tmtt) REVERT: C 1 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: C 181 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9170 (ptmm) REVERT: C 192 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: D 43 ASP cc_start: 0.9294 (t0) cc_final: 0.9006 (t0) REVERT: D 97 GLU cc_start: 0.9146 (pt0) cc_final: 0.8701 (mp0) REVERT: D 192 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8241 (tp30) REVERT: E 97 GLU cc_start: 0.9079 (pt0) cc_final: 0.8704 (mp0) REVERT: F 45 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8664 (tpp80) REVERT: F 73 ASP cc_start: 0.9080 (t0) cc_final: 0.8871 (t0) REVERT: H 73 ASP cc_start: 0.9071 (t0) cc_final: 0.8691 (t0) REVERT: I 45 ARG cc_start: 0.8407 (ttp80) cc_final: 0.7953 (tpp80) REVERT: I 73 ASP cc_start: 0.9045 (t0) cc_final: 0.8731 (t0) outliers start: 37 outliers final: 20 residues processed: 279 average time/residue: 0.7517 time to fit residues: 222.3758 Evaluate side-chains 266 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 58 optimal weight: 0.0040 chunk 21 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN F 62 ASN I 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.053057 restraints weight = 57172.418| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 3.74 r_work: 0.2411 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2397 r_free = 0.2397 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2397 r_free = 0.2397 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13841 Z= 0.163 Angle : 0.650 9.416 18847 Z= 0.325 Chirality : 0.042 0.196 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.268 115.222 2242 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.82 % Allowed : 26.83 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1630 helix: 1.78 (0.77), residues: 50 sheet: -0.24 (0.19), residues: 650 loop : -1.16 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.010 0.001 TYR C 117 PHE 0.011 0.001 PHE C 2 TRP 0.047 0.002 TRP E 133 HIS 0.002 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00378 (13805) covalent geometry : angle 0.62743 (18755) SS BOND : bond 0.00316 ( 16) SS BOND : angle 0.83522 ( 32) hydrogen bonds : bond 0.02907 ( 421) hydrogen bonds : angle 5.08066 ( 1230) link_BETA1-4 : bond 0.01154 ( 5) link_BETA1-4 : angle 4.78740 ( 15) link_NAG-ASN : bond 0.00225 ( 15) link_NAG-ASN : angle 2.17979 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.385 Fit side-chains REVERT: A 75 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9177 (mtmm) REVERT: A 97 GLU cc_start: 0.9059 (pt0) cc_final: 0.8673 (mp0) REVERT: A 191 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8153 (tmtt) REVERT: C 1 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: C 181 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9172 (ptmm) REVERT: C 192 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: D 43 ASP cc_start: 0.9284 (t0) cc_final: 0.9025 (t0) REVERT: D 97 GLU cc_start: 0.9123 (pt0) cc_final: 0.8689 (mp0) REVERT: E 97 GLU cc_start: 0.9075 (pt0) cc_final: 0.8694 (mp0) REVERT: F 43 LYS cc_start: 0.9285 (ttmm) cc_final: 0.9053 (mppt) REVERT: F 45 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8623 (tpp80) REVERT: F 73 ASP cc_start: 0.9070 (t0) cc_final: 0.8659 (t0) REVERT: G 87 LYS cc_start: 0.9369 (mttt) cc_final: 0.9110 (ptpt) REVERT: H 3 GLN cc_start: 0.8830 (mt0) cc_final: 0.8612 (tt0) REVERT: H 73 ASP cc_start: 0.9067 (t0) cc_final: 0.8709 (t0) REVERT: I 45 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8035 (tpp80) REVERT: I 73 ASP cc_start: 0.9062 (t0) cc_final: 0.8718 (t0) outliers start: 40 outliers final: 24 residues processed: 276 average time/residue: 0.7189 time to fit residues: 210.8318 Evaluate side-chains 259 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 0.0000 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.052711 restraints weight = 60529.428| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.77 r_work: 0.2400 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2384 r_free = 0.2384 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13841 Z= 0.170 Angle : 0.653 7.815 18847 Z= 0.328 Chirality : 0.042 0.195 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.245 115.364 2242 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.61 % Allowed : 27.25 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1630 helix: 1.63 (0.76), residues: 50 sheet: -0.25 (0.19), residues: 650 loop : -1.15 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.015 0.001 TYR D 128 PHE 0.011 0.001 PHE D 2 TRP 0.045 0.002 TRP E 133 HIS 0.002 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00398 (13805) covalent geometry : angle 0.63028 (18755) SS BOND : bond 0.00335 ( 16) SS BOND : angle 0.95433 ( 32) hydrogen bonds : bond 0.02948 ( 421) hydrogen bonds : angle 5.10106 ( 1230) link_BETA1-4 : bond 0.01070 ( 5) link_BETA1-4 : angle 4.78490 ( 15) link_NAG-ASN : bond 0.00261 ( 15) link_NAG-ASN : angle 2.12645 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.358 Fit side-chains REVERT: A 75 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9187 (mtmm) REVERT: A 97 GLU cc_start: 0.9061 (pt0) cc_final: 0.8680 (mp0) REVERT: A 191 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8137 (tmtt) REVERT: B 172 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: C 1 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: C 181 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.9178 (ptmm) REVERT: C 192 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: D 97 GLU cc_start: 0.9116 (pt0) cc_final: 0.8668 (mp0) REVERT: E 97 GLU cc_start: 0.9081 (pt0) cc_final: 0.8699 (mp0) REVERT: F 43 LYS cc_start: 0.9292 (ttmm) cc_final: 0.9048 (mppt) REVERT: F 73 ASP cc_start: 0.9085 (t0) cc_final: 0.8651 (t0) REVERT: H 3 GLN cc_start: 0.8847 (mt0) cc_final: 0.8625 (tt0) REVERT: H 73 ASP cc_start: 0.9055 (t0) cc_final: 0.8851 (t0) REVERT: I 45 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8055 (tpp80) REVERT: I 73 ASP cc_start: 0.9074 (t0) cc_final: 0.8737 (t0) outliers start: 37 outliers final: 23 residues processed: 278 average time/residue: 0.7204 time to fit residues: 212.5995 Evaluate side-chains 266 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 120 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.052655 restraints weight = 60947.569| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.82 r_work: 0.2397 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2393 r_free = 0.2393 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2393 r_free = 0.2393 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13841 Z= 0.171 Angle : 0.658 7.863 18847 Z= 0.330 Chirality : 0.042 0.192 2010 Planarity : 0.005 0.064 2410 Dihedral : 10.218 115.188 2242 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.46 % Allowed : 27.46 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1630 helix: 1.61 (0.76), residues: 50 sheet: -0.21 (0.19), residues: 645 loop : -1.17 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.010 0.001 TYR C 117 PHE 0.011 0.001 PHE D 2 TRP 0.044 0.002 TRP E 133 HIS 0.002 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00399 (13805) covalent geometry : angle 0.63549 (18755) SS BOND : bond 0.00337 ( 16) SS BOND : angle 1.00479 ( 32) hydrogen bonds : bond 0.02940 ( 421) hydrogen bonds : angle 5.09153 ( 1230) link_BETA1-4 : bond 0.01104 ( 5) link_BETA1-4 : angle 4.76424 ( 15) link_NAG-ASN : bond 0.00253 ( 15) link_NAG-ASN : angle 2.13040 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.332 Fit side-chains REVERT: A 75 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9173 (mtmm) REVERT: A 97 GLU cc_start: 0.9079 (pt0) cc_final: 0.8683 (mp0) REVERT: A 191 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8126 (tmtt) REVERT: B 172 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: C 1 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: C 181 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9184 (ptmm) REVERT: C 192 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8131 (tp30) REVERT: D 97 GLU cc_start: 0.9128 (pt0) cc_final: 0.8672 (mp0) REVERT: E 97 GLU cc_start: 0.9087 (pt0) cc_final: 0.8701 (mp0) REVERT: F 73 ASP cc_start: 0.9092 (t0) cc_final: 0.8646 (t0) REVERT: G 65 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8856 (mmtm) REVERT: H 3 GLN cc_start: 0.8845 (mt0) cc_final: 0.8573 (tt0) REVERT: H 85 ASN cc_start: 0.9212 (p0) cc_final: 0.8850 (p0) REVERT: I 45 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8046 (tpp80) REVERT: I 73 ASP cc_start: 0.9090 (t0) cc_final: 0.8758 (t0) REVERT: J 73 ASP cc_start: 0.9028 (t0) cc_final: 0.8754 (t0) outliers start: 35 outliers final: 24 residues processed: 270 average time/residue: 0.7375 time to fit residues: 211.5298 Evaluate side-chains 270 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 152 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 54 optimal weight: 0.0030 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.055287 restraints weight = 43485.510| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.38 r_work: 0.2474 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13841 Z= 0.121 Angle : 0.637 7.911 18847 Z= 0.321 Chirality : 0.041 0.184 2010 Planarity : 0.005 0.062 2410 Dihedral : 10.035 114.717 2242 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.18 % Allowed : 28.03 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.19), residues: 1630 helix: 2.54 (0.75), residues: 45 sheet: -0.12 (0.19), residues: 645 loop : -1.20 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.015 0.001 TYR D 128 PHE 0.008 0.001 PHE E 2 TRP 0.040 0.001 TRP E 133 HIS 0.001 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00287 (13805) covalent geometry : angle 0.61697 (18755) SS BOND : bond 0.00285 ( 16) SS BOND : angle 0.84182 ( 32) hydrogen bonds : bond 0.02578 ( 421) hydrogen bonds : angle 4.91165 ( 1230) link_BETA1-4 : bond 0.01277 ( 5) link_BETA1-4 : angle 4.57588 ( 15) link_NAG-ASN : bond 0.00192 ( 15) link_NAG-ASN : angle 1.97284 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.441 Fit side-chains REVERT: A 97 GLU cc_start: 0.9019 (pt0) cc_final: 0.8641 (mp0) REVERT: A 191 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8126 (tmtt) REVERT: B 172 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: C 97 GLU cc_start: 0.9007 (pt0) cc_final: 0.8646 (mp0) REVERT: C 181 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9154 (ptmm) REVERT: C 192 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: E 97 GLU cc_start: 0.9038 (pt0) cc_final: 0.8671 (mp0) REVERT: F 43 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9060 (mppt) REVERT: F 73 ASP cc_start: 0.9048 (t0) cc_final: 0.8630 (t0) REVERT: F 87 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9086 (ptpt) REVERT: G 87 LYS cc_start: 0.9325 (mttt) cc_final: 0.9058 (ptpt) REVERT: H 3 GLN cc_start: 0.8811 (mt0) cc_final: 0.8580 (tt0) REVERT: H 73 ASP cc_start: 0.8911 (t0) cc_final: 0.8706 (t0) REVERT: H 85 ASN cc_start: 0.9166 (p0) cc_final: 0.8806 (p0) REVERT: I 45 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8019 (tpp80) REVERT: I 73 ASP cc_start: 0.9049 (t0) cc_final: 0.8734 (t0) REVERT: J 19 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8440 (ttt-90) REVERT: J 73 ASP cc_start: 0.8989 (t0) cc_final: 0.8696 (t0) outliers start: 31 outliers final: 19 residues processed: 276 average time/residue: 0.7745 time to fit residues: 226.9188 Evaluate side-chains 267 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN I 77 ASN J 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.053500 restraints weight = 58578.317| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 3.75 r_work: 0.2417 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2402 r_free = 0.2402 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2402 r_free = 0.2402 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13841 Z= 0.166 Angle : 0.659 7.716 18847 Z= 0.330 Chirality : 0.042 0.193 2010 Planarity : 0.005 0.063 2410 Dihedral : 10.098 115.021 2242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.25 % Allowed : 27.96 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.19), residues: 1630 helix: 1.52 (0.77), residues: 50 sheet: -0.17 (0.19), residues: 645 loop : -1.12 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 204 TYR 0.009 0.001 TYR C 117 PHE 0.011 0.001 PHE D 2 TRP 0.038 0.002 TRP E 133 HIS 0.002 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00389 (13805) covalent geometry : angle 0.63866 (18755) SS BOND : bond 0.00321 ( 16) SS BOND : angle 0.93183 ( 32) hydrogen bonds : bond 0.02874 ( 421) hydrogen bonds : angle 4.97861 ( 1230) link_BETA1-4 : bond 0.01117 ( 5) link_BETA1-4 : angle 4.62029 ( 15) link_NAG-ASN : bond 0.00267 ( 15) link_NAG-ASN : angle 2.00709 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.77 seconds wall clock time: 84 minutes 39.77 seconds (5079.77 seconds total)