Starting phenix.real_space_refine on Fri Jul 3 09:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ce4_16598/07_2026/8ce4_16598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce4_16598/07_2026/8ce4_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_16598/07_2026/8ce4_16598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2026/8ce4_16598.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2026/8ce4_16598.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2026/8ce4_16598.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2026/8ce4_16598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2026/8ce4_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.73, per 1000 atoms: 0.35 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: 1.13 Conformation dependent library (CDL) restraints added in 897.4 milliseconds 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: 0.59 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: 2.13 Time building geometry restraints manager: 1.42 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 - 17.73: 6743 17.73 - 35.47: 860 35.47 - 53.20: 266 53.20 - 70.94: 70 70.94 - 88.67: 19 Dihedral angle restraints: 7958 sinusoidal: 3183 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 7955 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.970 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 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 : 17.954 88.671 4860 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 are 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/Z covalent geometry : bond 0.00424 / 0.17 (13805) covalent geometry : angle 0.62555 / 0.33 (18755) SS BOND : bond 0.00437 / 0.24 ( 16) SS BOND : angle 0.76058 / 0.45 ( 32) hydrogen bonds : bond 0.13933 / 9.08 ( 421) hydrogen bonds : angle 6.67362 / 4.73 ( 1230) link_BETA1-4 : bond 0.01127 / 0.60 ( 5) link_BETA1-4 : angle 5.20246 / 2.99 ( 15) link_NAG-ASN : bond 0.00164 / 0.10 ( 15) link_NAG-ASN : angle 2.03378 / 1.25 ( 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 : 0.652 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: 0.8318 time to fit residues: 284.6984 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 : 0.543 ------------------------------------------------------------------------------- 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... 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 = 0.3004 r_free = 0.3004 target = 0.072979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.052645 restraints weight = 33220.450| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 2.98 r_work: 0.2414 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2271 r_free = 0.2271 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2270 r_free = 0.2270 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9287 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13841 Z= 0.278 Angle : 0.689 8.686 18847 Z= 0.351 Chirality : 0.044 0.299 2010 Planarity : 0.007 0.100 2410 Dihedral : 6.274 56.174 1849 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 4.44 % Allowed : 24.08 % Favored : 71.48 % 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 are not related in a simple way. whole: -0.86 (0.19), residues: 1630 helix: 1.87 (0.73), residues: 50 sheet: -0.28 (0.19), residues: 655 loop : -0.90 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 108 TYR 0.015 0.002 TYR A 117 PHE 0.017 0.002 PHE C 2 TRP 0.018 0.002 TRP B 133 HIS 0.004 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 (13805) covalent geometry : angle 0.67005 / 0.35 (18755) SS BOND : bond 0.00457 / 0.24 ( 16) SS BOND : angle 0.93038 / 0.57 ( 32) hydrogen bonds : bond 0.03916 / 2.57 ( 421) hydrogen bonds : angle 5.64591 / 3.95 ( 1230) link_BETA1-4 : bond 0.01274 / 0.70 ( 5) link_BETA1-4 : angle 4.17348 / 2.35 ( 15) link_NAG-ASN : bond 0.00376 / 0.21 ( 15) link_NAG-ASN : angle 2.28551 / 1.46 ( 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 324 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.681 Fit side-chains REVERT: A 191 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8145 (tmtt) REVERT: G 13 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7236 (mm110) REVERT: H 73 ASP cc_start: 0.9102 (t0) cc_final: 0.8809 (t0) REVERT: I 73 ASP cc_start: 0.9054 (t0) cc_final: 0.8797 (t0) REVERT: J 13 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7102 (mm110) REVERT: J 84 ASN cc_start: 0.8290 (m-40) cc_final: 0.7927 (m-40) outliers start: 63 outliers final: 26 residues processed: 309 average time/residue: 0.8305 time to fit residues: 273.1251 Evaluate side-chains 273 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 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: 0.3980 chunk 85 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 I 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.053537 restraints weight = 63742.469| |-----------------------------------------------------------------------------| r_work (start): 0.2571 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: 0.2410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2410 r_free = 0.2410 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13841 Z= 0.141 Angle : 0.620 7.689 18847 Z= 0.316 Chirality : 0.042 0.247 2010 Planarity : 0.005 0.084 2410 Dihedral : 5.190 59.224 1832 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.66 % Allowed : 24.65 % 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 are not related in a simple way. whole: -0.94 (0.19), residues: 1630 helix: 2.91 (0.73), residues: 45 sheet: -0.24 (0.19), residues: 650 loop : -1.08 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 132 TYR 0.014 0.001 TYR B 117 PHE 0.016 0.001 PHE E 136 TRP 0.029 0.001 TRP B 133 HIS 0.001 0.000 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13805) covalent geometry : angle 0.59990 / 0.31 (18755) SS BOND : bond 0.00363 / 0.18 ( 16) SS BOND : angle 0.71194 / 0.42 ( 32) hydrogen bonds : bond 0.03132 / 2.07 ( 421) hydrogen bonds : angle 5.32476 / 3.72 ( 1230) link_BETA1-4 : bond 0.01518 / 0.81 ( 5) link_BETA1-4 : angle 4.00548 / 2.25 ( 15) link_NAG-ASN : bond 0.00179 / 0.10 ( 15) link_NAG-ASN : angle 2.27448 / 1.45 ( 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 308 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 0.574 Fit side-chains REVERT: A 75 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9179 (mtmm) REVERT: A 191 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8179 (tmtt) REVERT: B 97 GLU cc_start: 0.9083 (pt0) cc_final: 0.8785 (mp0) REVERT: C 97 GLU cc_start: 0.9065 (pt0) cc_final: 0.8729 (mp0) REVERT: D 97 GLU cc_start: 0.9170 (pt0) cc_final: 0.8779 (mp0) REVERT: D 192 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: E 97 GLU cc_start: 0.9087 (pt0) cc_final: 0.8714 (mp0) REVERT: F 13 GLN cc_start: 0.7576 (mm-40) cc_final: 0.6867 (mm110) REVERT: H 13 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7012 (mm110) REVERT: H 73 ASP cc_start: 0.9046 (t0) cc_final: 0.8710 (t0) REVERT: I 13 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6796 (mm110) REVERT: I 45 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8152 (ttp80) REVERT: I 73 ASP cc_start: 0.8992 (t0) cc_final: 0.8601 (t0) REVERT: J 121 THR cc_start: 0.9490 (m) cc_final: 0.9084 (p) outliers start: 52 outliers final: 21 residues processed: 296 average time/residue: 0.7897 time to fit residues: 248.4075 Evaluate side-chains 276 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3043 r_free = 0.3043 target = 0.074817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.053564 restraints weight = 58618.610| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 3.74 r_work: 0.2419 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2414 r_free = 0.2414 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 = 0.2414 r_free = 0.2414 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13841 Z= 0.153 Angle : 0.618 7.502 18847 Z= 0.314 Chirality : 0.041 0.223 2010 Planarity : 0.005 0.076 2410 Dihedral : 4.913 58.137 1826 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.45 % Allowed : 24.86 % 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 are not related in a simple way. whole: -0.97 (0.19), residues: 1630 helix: 2.01 (0.76), residues: 50 sheet: -0.21 (0.19), residues: 650 loop : -1.12 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 204 TYR 0.013 0.001 TYR B 117 PHE 0.011 0.001 PHE C 2 TRP 0.029 0.001 TRP D 133 HIS 0.002 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13805) covalent geometry : angle 0.59794 / 0.31 (18755) SS BOND : bond 0.00326 / 0.17 ( 16) SS BOND : angle 0.75916 / 0.45 ( 32) hydrogen bonds : bond 0.02978 / 1.96 ( 421) hydrogen bonds : angle 5.18569 / 3.62 ( 1230) link_BETA1-4 : bond 0.01424 / 0.77 ( 5) link_BETA1-4 : angle 3.96830 / 2.23 ( 15) link_NAG-ASN : bond 0.00219 / 0.12 ( 15) link_NAG-ASN : angle 2.27258 / 1.45 ( 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 307 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 0.618 Fit side-chains REVERT: A 75 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9180 (mtmm) REVERT: A 97 GLU cc_start: 0.9048 (pt0) cc_final: 0.8716 (mp0) REVERT: A 172 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8779 (tt0) REVERT: A 191 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8189 (tmtt) REVERT: B 97 GLU cc_start: 0.9056 (pt0) cc_final: 0.8752 (mp0) REVERT: B 192 GLU cc_start: 0.8439 (tp30) cc_final: 0.8185 (tp30) REVERT: C 192 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: D 97 GLU cc_start: 0.9156 (pt0) cc_final: 0.8772 (mp0) REVERT: D 192 GLU cc_start: 0.8429 (tp30) cc_final: 0.8134 (tp30) REVERT: E 97 GLU cc_start: 0.9066 (pt0) cc_final: 0.8715 (mp0) REVERT: H 73 ASP cc_start: 0.9064 (t0) cc_final: 0.8710 (t0) REVERT: I 73 ASP cc_start: 0.9027 (t0) cc_final: 0.8679 (t0) REVERT: J 45 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8382 (tpp80) outliers start: 49 outliers final: 21 residues processed: 295 average time/residue: 0.8351 time to fit residues: 261.7242 Evaluate side-chains 275 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain C residue 176 VAL 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 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 16 ASP 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: 0.9980 chunk 58 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 159 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3038 r_free = 0.3038 target = 0.074442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.053091 restraints weight = 57173.124| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 3.73 r_work: 0.2412 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2412 ------------------------------------------------------------------------------- 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 = 0.46 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 moved from start: 0.1844 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= 0.165 Angle : 0.621 7.414 18847 Z= 0.316 Chirality : 0.042 0.207 2010 Planarity : 0.005 0.072 2410 Dihedral : 4.875 56.327 1825 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.59 % Allowed : 25.14 % 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 are not related in a simple way. whole: -1.01 (0.19), residues: 1630 helix: 1.95 (0.77), residues: 50 sheet: -0.20 (0.19), residues: 650 loop : -1.17 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 204 TYR 0.011 0.001 TYR A 128 PHE 0.012 0.001 PHE C 2 TRP 0.048 0.002 TRP E 133 HIS 0.002 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13805) covalent geometry : angle 0.60239 / 0.31 (18755) SS BOND : bond 0.00329 / 0.17 ( 16) SS BOND : angle 0.76445 / 0.45 ( 32) hydrogen bonds : bond 0.02965 / 1.95 ( 421) hydrogen bonds : angle 5.13125 / 3.58 ( 1230) link_BETA1-4 : bond 0.01424 / 0.77 ( 5) link_BETA1-4 : angle 3.94196 / 2.21 ( 15) link_NAG-ASN : bond 0.00211 / 0.12 ( 15) link_NAG-ASN : angle 2.18524 / 1.40 ( 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 303 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.332 Fit side-chains REVERT: A 75 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9194 (mtmm) REVERT: A 97 GLU cc_start: 0.9096 (pt0) cc_final: 0.8741 (mp0) REVERT: A 172 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8783 (tt0) REVERT: A 191 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8191 (tmtt) REVERT: A 205 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8092 (ttp-170) REVERT: B 97 GLU cc_start: 0.9082 (pt0) cc_final: 0.8758 (mp0) REVERT: C 1 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: C 181 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9165 (ptmm) REVERT: C 192 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: D 40 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9026 (mtm) REVERT: D 97 GLU cc_start: 0.9150 (pt0) cc_final: 0.8729 (mp0) REVERT: D 192 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: E 97 GLU cc_start: 0.9083 (pt0) cc_final: 0.8729 (mp0) REVERT: F 43 LYS cc_start: 0.9278 (ttmm) cc_final: 0.9041 (mppt) REVERT: H 73 ASP cc_start: 0.9070 (t0) cc_final: 0.8682 (t0) REVERT: I 73 ASP cc_start: 0.9029 (t0) cc_final: 0.8718 (t0) outliers start: 51 outliers final: 23 residues processed: 290 average time/residue: 0.7674 time to fit residues: 236.5408 Evaluate side-chains 272 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 40 MET 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 65 LYS 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 43 LYS Chi-restraints excluded: chain J residue 65 LYS 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: 0.6980 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 F 62 ASN G 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 = 0.3033 r_free = 0.3033 target = 0.074040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.052656 restraints weight = 58640.736| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.76 r_work: 0.2401 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2386 r_free = 0.2386 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 = 0.2386 r_free = 0.2386 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9236 moved from start: 0.1941 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= 0.179 Angle : 0.640 8.043 18847 Z= 0.324 Chirality : 0.042 0.202 2010 Planarity : 0.005 0.069 2410 Dihedral : 4.917 55.537 1824 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.03 % Allowed : 26.27 % 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 are not related in a simple way. whole: -1.06 (0.19), residues: 1630 helix: 1.83 (0.77), residues: 50 sheet: -0.23 (0.19), residues: 650 loop : -1.20 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 204 TYR 0.012 0.001 TYR D 128 PHE 0.012 0.001 PHE C 2 TRP 0.052 0.002 TRP E 133 HIS 0.002 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (13805) covalent geometry : angle 0.62207 / 0.32 (18755) SS BOND : bond 0.00328 / 0.17 ( 16) SS BOND : angle 0.79313 / 0.48 ( 32) hydrogen bonds : bond 0.03027 / 2.00 ( 421) hydrogen bonds : angle 5.14459 / 3.60 ( 1230) link_BETA1-4 : bond 0.01366 / 0.74 ( 5) link_BETA1-4 : angle 3.94005 / 2.20 ( 15) link_NAG-ASN : bond 0.00232 / 0.13 ( 15) link_NAG-ASN : angle 2.16692 / 1.40 ( 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 290 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.500 Fit side-chains REVERT: A 75 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9185 (mtmm) REVERT: A 97 GLU cc_start: 0.9084 (pt0) cc_final: 0.8728 (mp0) REVERT: A 172 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8790 (tt0) REVERT: A 191 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8166 (tmtt) REVERT: C 1 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: C 181 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9176 (ptmm) REVERT: D 40 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9041 (mtm) REVERT: D 97 GLU cc_start: 0.9135 (pt0) cc_final: 0.8705 (mp0) REVERT: E 97 GLU cc_start: 0.9062 (pt0) cc_final: 0.8716 (mp0) REVERT: H 73 ASP cc_start: 0.9073 (t0) cc_final: 0.8683 (t0) REVERT: I 45 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7948 (tpp80) REVERT: I 73 ASP cc_start: 0.9055 (t0) cc_final: 0.8734 (t0) REVERT: J 73 ASP cc_start: 0.9059 (t0) cc_final: 0.8832 (t0) outliers start: 43 outliers final: 21 residues processed: 279 average time/residue: 0.8216 time to fit residues: 243.9359 Evaluate side-chains 267 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 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 65 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: 1.9990 chunk 131 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 124 optimal weight: 6.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.071514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.050202 restraints weight = 57153.520| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 3.66 r_work: 0.2356 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2354 r_free = 0.2354 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2354 r_free = 0.2354 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9259 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13841 Z= 0.269 Angle : 0.686 7.262 18847 Z= 0.348 Chirality : 0.044 0.207 2010 Planarity : 0.005 0.069 2410 Dihedral : 5.006 36.809 1822 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.89 % Allowed : 26.76 % 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 are not related in a simple way. whole: -1.12 (0.19), residues: 1630 helix: 1.59 (0.76), residues: 50 sheet: -0.29 (0.19), residues: 645 loop : -1.20 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 204 TYR 0.012 0.001 TYR A 128 PHE 0.016 0.002 PHE D 2 TRP 0.046 0.002 TRP E 133 HIS 0.004 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.27 (13805) covalent geometry : angle 0.66631 / 0.34 (18755) SS BOND : bond 0.00442 / 0.24 ( 16) SS BOND : angle 1.00557 / 0.61 ( 32) hydrogen bonds : bond 0.03482 / 2.30 ( 421) hydrogen bonds : angle 5.37275 / 3.75 ( 1230) link_BETA1-4 : bond 0.01200 / 0.66 ( 5) link_BETA1-4 : angle 4.12142 / 2.30 ( 15) link_NAG-ASN : bond 0.00318 / 0.17 ( 15) link_NAG-ASN : angle 2.34322 / 1.51 ( 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 285 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.577 Fit side-chains REVERT: A 75 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9218 (mtmm) REVERT: A 97 GLU cc_start: 0.9083 (pt0) cc_final: 0.8725 (mp0) REVERT: A 191 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8139 (tmtt) REVERT: B 97 GLU cc_start: 0.9102 (pt0) cc_final: 0.8738 (mp0) REVERT: B 172 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: C 1 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: C 181 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9183 (ptmm) REVERT: D 40 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.9041 (mtm) REVERT: D 97 GLU cc_start: 0.9136 (pt0) cc_final: 0.8691 (mp0) REVERT: E 97 GLU cc_start: 0.9079 (pt0) cc_final: 0.8719 (mp0) REVERT: F 43 LYS cc_start: 0.9337 (ttmm) cc_final: 0.9048 (mppt) REVERT: F 73 ASP cc_start: 0.9098 (t0) cc_final: 0.8886 (t0) REVERT: H 3 GLN cc_start: 0.8859 (mt0) cc_final: 0.8643 (tt0) REVERT: H 73 ASP cc_start: 0.9086 (t0) cc_final: 0.8670 (t0) REVERT: I 45 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7992 (tpp80) REVERT: I 73 ASP cc_start: 0.9086 (t0) cc_final: 0.8747 (t0) REVERT: J 73 ASP cc_start: 0.9101 (t0) cc_final: 0.8867 (t0) outliers start: 41 outliers final: 25 residues processed: 274 average time/residue: 0.8518 time to fit residues: 248.4220 Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 93 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.072849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.051397 restraints weight = 60289.914| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 3.77 r_work: 0.2378 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2375 r_free = 0.2375 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2375 r_free = 0.2375 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9247 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13841 Z= 0.194 Angle : 0.666 7.889 18847 Z= 0.338 Chirality : 0.043 0.193 2010 Planarity : 0.005 0.065 2410 Dihedral : 4.874 36.435 1822 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.61 % Allowed : 27.11 % Favored : 70.28 % 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 are not related in a simple way. whole: -1.14 (0.19), residues: 1630 helix: 1.59 (0.77), residues: 50 sheet: -0.33 (0.19), residues: 645 loop : -1.20 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 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 0.003 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (13805) covalent geometry : angle 0.64779 / 0.33 (18755) SS BOND : bond 0.00364 / 0.19 ( 16) SS BOND : angle 0.90111 / 0.54 ( 32) hydrogen bonds : bond 0.03081 / 2.03 ( 421) hydrogen bonds : angle 5.26811 / 3.68 ( 1230) link_BETA1-4 : bond 0.01428 / 0.77 ( 5) link_BETA1-4 : angle 3.99110 / 2.21 ( 15) link_NAG-ASN : bond 0.00223 / 0.13 ( 15) link_NAG-ASN : angle 2.29321 / 1.48 ( 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 285 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.448 Fit side-chains REVERT: A 75 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9223 (mtmm) REVERT: A 97 GLU cc_start: 0.9092 (pt0) cc_final: 0.8739 (mp0) REVERT: A 191 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8131 (tmtt) REVERT: C 1 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: C 181 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.9166 (ptmm) REVERT: D 40 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.9062 (mtm) REVERT: D 97 GLU cc_start: 0.9140 (pt0) cc_final: 0.8700 (mp0) REVERT: D 205 ARG cc_start: 0.8703 (ttp-170) cc_final: 0.8134 (ttp-170) REVERT: E 97 GLU cc_start: 0.9073 (pt0) cc_final: 0.8706 (mp0) REVERT: F 73 ASP cc_start: 0.9093 (t0) cc_final: 0.8683 (t0) REVERT: G 65 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8917 (mmtm) REVERT: H 3 GLN cc_start: 0.8847 (mt0) cc_final: 0.8593 (tt0) REVERT: H 73 ASP cc_start: 0.9084 (t0) cc_final: 0.8733 (t0) REVERT: H 85 ASN cc_start: 0.9252 (p0) cc_final: 0.8868 (p0) REVERT: I 45 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8055 (tpp80) REVERT: I 73 ASP cc_start: 0.9082 (t0) cc_final: 0.8760 (t0) REVERT: J 73 ASP cc_start: 0.9094 (t0) cc_final: 0.8866 (t0) outliers start: 37 outliers final: 24 residues processed: 276 average time/residue: 0.8217 time to fit residues: 241.6439 Evaluate side-chains 275 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 183 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 44 GLU 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 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 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: 3.9990 chunk 74 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.072459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.051023 restraints weight = 61021.904| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 3.78 r_work: 0.2346 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2355 r_free = 0.2355 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2355 r_free = 0.2355 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9258 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13841 Z= 0.228 Angle : 0.683 7.822 18847 Z= 0.346 Chirality : 0.043 0.198 2010 Planarity : 0.005 0.065 2410 Dihedral : 4.947 37.474 1822 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.68 % Allowed : 26.62 % 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 are not related in a simple way. whole: -1.14 (0.19), residues: 1630 helix: 1.52 (0.76), residues: 50 sheet: -0.36 (0.19), residues: 645 loop : -1.18 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.013 0.001 TYR A 128 PHE 0.013 0.001 PHE D 2 TRP 0.042 0.002 TRP E 133 HIS 0.003 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (13805) covalent geometry : angle 0.66393 / 0.34 (18755) SS BOND : bond 0.00417 / 0.23 ( 16) SS BOND : angle 1.15171 / 0.69 ( 32) hydrogen bonds : bond 0.03255 / 2.14 ( 421) hydrogen bonds : angle 5.31852 / 3.70 ( 1230) link_BETA1-4 : bond 0.01236 / 0.67 ( 5) link_BETA1-4 : angle 4.03555 / 2.25 ( 15) link_NAG-ASN : bond 0.00273 / 0.15 ( 15) link_NAG-ASN : angle 2.26812 / 1.48 ( 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 284 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.531 Fit side-chains REVERT: A 75 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.9255 (mtmm) REVERT: A 97 GLU cc_start: 0.9086 (pt0) cc_final: 0.8724 (mp0) REVERT: A 191 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8157 (tmtt) REVERT: B 172 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: C 1 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: C 181 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9191 (ptmm) REVERT: D 97 GLU cc_start: 0.9138 (pt0) cc_final: 0.8693 (mp0) REVERT: E 97 GLU cc_start: 0.9077 (pt0) cc_final: 0.8706 (mp0) REVERT: F 73 ASP cc_start: 0.9122 (t0) cc_final: 0.8673 (t0) REVERT: G 65 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8922 (mmtm) REVERT: H 3 GLN cc_start: 0.8866 (mt0) cc_final: 0.8601 (tt0) REVERT: H 73 ASP cc_start: 0.9078 (t0) cc_final: 0.8862 (t0) REVERT: H 85 ASN cc_start: 0.9283 (p0) cc_final: 0.8882 (p0) REVERT: I 45 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8060 (tpp80) REVERT: I 73 ASP cc_start: 0.9096 (t0) cc_final: 0.8774 (t0) REVERT: I 83 MET cc_start: 0.8333 (mtt) cc_final: 0.8036 (mtt) REVERT: J 45 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8465 (tpp80) REVERT: J 73 ASP cc_start: 0.9104 (t0) cc_final: 0.8885 (t0) outliers start: 38 outliers final: 25 residues processed: 275 average time/residue: 0.7939 time to fit residues: 232.5673 Evaluate side-chains 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 183 SER 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 G residue 44 GLU 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 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 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: 4.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 0.0040 chunk 54 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN B 3 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.074692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.053980 restraints weight = 43520.402| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 3.35 r_work: 0.2452 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9227 moved from start: 0.2154 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 : 0.651 8.195 18847 Z= 0.331 Chirality : 0.042 0.187 2010 Planarity : 0.005 0.064 2410 Dihedral : 4.698 35.816 1822 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.04 % Allowed : 27.61 % 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 are not related in a simple way. whole: -1.09 (0.19), residues: 1630 helix: 2.46 (0.75), residues: 45 sheet: -0.31 (0.19), residues: 650 loop : -1.19 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 204 TYR 0.016 0.001 TYR D 128 PHE 0.008 0.001 PHE C 2 TRP 0.041 0.001 TRP E 133 HIS 0.001 0.000 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (13805) covalent geometry : angle 0.63428 / 0.33 (18755) SS BOND : bond 0.00293 / 0.15 ( 16) SS BOND : angle 0.95664 / 0.56 ( 32) hydrogen bonds : bond 0.02738 / 1.80 ( 421) hydrogen bonds : angle 5.11835 / 3.56 ( 1230) link_BETA1-4 : bond 0.01467 / 0.79 ( 5) link_BETA1-4 : angle 3.80568 / 2.11 ( 15) link_NAG-ASN : bond 0.00173 / 0.10 ( 15) link_NAG-ASN : angle 2.14513 / 1.41 ( 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 275 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.613 Fit side-chains REVERT: A 97 GLU cc_start: 0.9042 (pt0) cc_final: 0.8680 (mp0) REVERT: A 191 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8172 (tmtt) REVERT: B 97 GLU cc_start: 0.9045 (pt0) cc_final: 0.8703 (mp0) REVERT: B 172 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: C 1 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: C 181 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9162 (ptmm) REVERT: D 97 GLU cc_start: 0.9079 (pt0) cc_final: 0.8678 (mp0) REVERT: E 97 GLU cc_start: 0.9036 (pt0) cc_final: 0.8682 (mp0) REVERT: F 73 ASP cc_start: 0.9075 (t0) cc_final: 0.8643 (t0) REVERT: G 65 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8850 (mmtm) REVERT: H 3 GLN cc_start: 0.8834 (mt0) cc_final: 0.8558 (tt0) REVERT: H 85 ASN cc_start: 0.9250 (p0) cc_final: 0.8837 (p0) REVERT: I 45 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8042 (tpp80) REVERT: I 73 ASP cc_start: 0.9057 (t0) cc_final: 0.8715 (t0) REVERT: J 45 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8519 (tpp80) REVERT: J 73 ASP cc_start: 0.9082 (t0) cc_final: 0.8816 (t0) outliers start: 29 outliers final: 20 residues processed: 268 average time/residue: 0.8785 time to fit residues: 250.5965 Evaluate side-chains 260 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS 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 G residue 65 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 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 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 170 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.052850 restraints weight = 58427.567| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 3.73 r_work: 0.2403 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2389 r_free = 0.2389 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 = 0.2389 r_free = 0.2389 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9235 moved from start: 0.2156 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= 0.165 Angle : 0.649 7.962 18847 Z= 0.330 Chirality : 0.042 0.189 2010 Planarity : 0.005 0.064 2410 Dihedral : 4.693 35.012 1822 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.90 % Allowed : 27.89 % Favored : 70.21 % 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 are not related in a simple way. whole: -1.07 (0.19), residues: 1630 helix: 1.53 (0.76), residues: 50 sheet: -0.27 (0.19), residues: 645 loop : -1.16 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 204 TYR 0.014 0.001 TYR A 128 PHE 0.010 0.001 PHE D 2 TRP 0.040 0.002 TRP C 133 HIS 0.002 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (13805) covalent geometry : angle 0.63239 / 0.33 (18755) SS BOND : bond 0.00333 / 0.18 ( 16) SS BOND : angle 0.98217 / 0.58 ( 32) hydrogen bonds : bond 0.02902 / 1.91 ( 421) hydrogen bonds : angle 5.11091 / 3.55 ( 1230) link_BETA1-4 : bond 0.01372 / 0.74 ( 5) link_BETA1-4 : angle 3.81310 / 2.13 ( 15) link_NAG-ASN : bond 0.00216 / 0.12 ( 15) link_NAG-ASN : angle 2.11214 / 1.39 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5630.42 seconds wall clock time: 96 minutes 43.10 seconds (5803.10 seconds total)