Starting phenix.real_space_refine on Thu May 15 16:55:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce4_16598/05_2025/8ce4_16598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce4_16598/05_2025/8ce4_16598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ce4_16598/05_2025/8ce4_16598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce4_16598/05_2025/8ce4_16598.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce4_16598/05_2025/8ce4_16598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce4_16598/05_2025/8ce4_16598.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13435 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "B" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "C" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "E" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "F" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.28, per 1000 atoms: 0.91 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: 3.15 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.88 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: 4.37 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4318 1.35 - 1.47: 3743 1.47 - 1.59: 5648 1.59 - 1.71: 1 1.71 - 1.83: 95 Bond restraints: 13805 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CB PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.24e+00 ... (remaining 13800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 18328 1.88 - 3.77: 366 3.77 - 5.65: 54 5.65 - 7.53: 5 7.53 - 9.42: 2 Bond angle restraints: 18755 Sorted by residual: angle pdb=" CA PRO F 88 " pdb=" N PRO F 88 " pdb=" CD PRO F 88 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.52e+01 angle pdb=" CA PRO D 169 " pdb=" N PRO D 169 " pdb=" CD PRO D 169 " ideal model delta sigma weight residual 112.00 104.69 7.31 1.40e+00 5.10e-01 2.73e+01 angle pdb=" C TRP E 133 " pdb=" N PHE E 134 " pdb=" CA PHE E 134 " ideal model delta sigma weight residual 121.80 130.64 -8.84 2.44e+00 1.68e-01 1.31e+01 angle pdb=" N PRO F 88 " pdb=" CD PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 103.20 98.02 5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 112.00 107.83 4.17 1.40e+00 5.10e-01 8.87e+00 ... (remaining 18750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 7563 25.07 - 50.15: 656 50.15 - 75.22: 137 75.22 - 100.29: 14 100.29 - 125.36: 8 Dihedral angle restraints: 8378 sinusoidal: 3603 harmonic: 4775 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " pdb=" SG CYS H 114 " pdb=" CB CYS H 114 " ideal model delta sinusoidal sigma weight residual 93.00 35.04 57.96 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS I 95 " pdb=" SG CYS I 95 " pdb=" SG CYS I 114 " pdb=" CB CYS I 114 " ideal model delta sinusoidal sigma weight residual 93.00 37.20 55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 8375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1541 0.044 - 0.087: 344 0.087 - 0.131: 113 0.131 - 0.175: 9 0.175 - 0.218: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 178 " pdb=" CA ILE A 178 " pdb=" CG1 ILE A 178 " pdb=" CG2 ILE A 178 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CB ILE E 178 " pdb=" CA ILE E 178 " pdb=" CG1 ILE E 178 " pdb=" CG2 ILE E 178 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2007 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 168 " -0.096 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO D 169 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 87 " -0.069 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO F 88 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 168 " 0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO B 169 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " 0.050 5.00e-02 4.00e+02 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 474 2.71 - 3.26: 12004 3.26 - 3.80: 22376 3.80 - 4.35: 30099 4.35 - 4.90: 49427 Nonbonded interactions: 114380 Sorted by model distance: nonbonded pdb=" O TYR I 32 " pdb=" NH2 ARG I 72 " model vdw 2.159 3.120 nonbonded pdb=" O TYR G 32 " pdb=" NH2 ARG G 72 " model vdw 2.170 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 72 " model vdw 2.174 3.120 nonbonded pdb=" O TYR F 32 " pdb=" NH2 ARG F 72 " model vdw 2.175 3.120 nonbonded pdb=" O TYR J 32 " pdb=" NH2 ARG J 72 " model vdw 2.186 3.120 ... (remaining 114375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.260 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 13841 Z= 0.174 Angle : 0.649 11.167 18847 Z= 0.334 Chirality : 0.043 0.218 2010 Planarity : 0.007 0.140 2410 Dihedral : 18.891 125.364 5280 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 2.61 % Allowed : 26.69 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (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 TRP 0.013 0.001 TRP A 153 HIS 0.002 0.001 HIS B 104 PHE 0.020 0.001 PHE A 136 TYR 0.019 0.001 TYR E 128 ARG 0.006 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 15) link_NAG-ASN : angle 2.03378 ( 45) link_BETA1-4 : bond 0.01127 ( 5) link_BETA1-4 : angle 5.20246 ( 15) hydrogen bonds : bond 0.13933 ( 421) hydrogen bonds : angle 6.67362 ( 1230) SS BOND : bond 0.00437 ( 16) SS BOND : angle 0.76058 ( 32) covalent geometry : bond 0.00424 (13805) covalent geometry : angle 0.62555 (18755) *********************** 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 : 1.531 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: 1.6618 time to fit residues: 568.4867 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 : 1.419 ------------------------------------------------------------------------------- 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 135 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 56 GLN B 3 GLN B 46 ASN C 26 GLN C 46 ASN C 116 GLN D 46 ASN E 46 ASN F 13 GLN G 13 GLN H 13 GLN I 13 GLN I 84 ASN J 5 GLN J 13 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.054614 restraints weight = 53495.213| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 3.65 r_work: 0.2447 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2442 r_free = 0.2442 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1388 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= 0.151 Angle : 0.651 8.839 18847 Z= 0.328 Chirality : 0.042 0.282 2010 Planarity : 0.006 0.097 2410 Dihedral : 11.680 114.639 2269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 4.01 % Allowed : 24.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1630 helix: 1.99 (0.74), residues: 50 sheet: -0.17 (0.19), residues: 650 loop : -0.96 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 133 HIS 0.002 0.001 HIS D 62 PHE 0.014 0.001 PHE A 136 TYR 0.016 0.001 TYR B 117 ARG 0.006 0.001 ARG G 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 15) link_NAG-ASN : angle 2.14222 ( 45) link_BETA1-4 : bond 0.01263 ( 5) link_BETA1-4 : angle 4.98150 ( 15) hydrogen bonds : bond 0.03275 ( 421) hydrogen bonds : angle 5.42515 ( 1230) SS BOND : bond 0.00335 ( 16) SS BOND : angle 0.77156 ( 32) covalent geometry : bond 0.00351 (13805) covalent geometry : angle 0.62755 (18755) *********************** 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 325 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 1.408 Fit side-chains REVERT: A 75 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9143 (mtmm) REVERT: A 191 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8149 (tmtt) REVERT: B 98 ARG cc_start: 0.9196 (mtm180) cc_final: 0.8951 (mtm180) REVERT: F 13 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7083 (mm110) REVERT: G 13 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7230 (mm110) REVERT: H 13 GLN cc_start: 0.7716 (mm-40) cc_final: 0.6968 (mm110) REVERT: H 73 ASP cc_start: 0.9002 (t0) cc_final: 0.8727 (t0) REVERT: H 84 ASN cc_start: 0.7975 (m-40) cc_final: 0.7558 (m110) REVERT: I 13 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7144 (mm110) REVERT: I 73 ASP cc_start: 0.8935 (t0) cc_final: 0.8691 (t0) REVERT: J 13 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7037 (mm110) REVERT: J 121 THR cc_start: 0.9512 (m) cc_final: 0.9077 (p) outliers start: 57 outliers final: 22 residues processed: 310 average time/residue: 1.7551 time to fit residues: 578.7317 Evaluate side-chains 278 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 26 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 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 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN E 46 ASN F 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.072123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.050777 restraints weight = 58794.819| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 3.70 r_work: 0.2362 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2349 r_free = 0.2349 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2349 r_free = 0.2349 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13841 Z= 0.273 Angle : 0.685 8.470 18847 Z= 0.344 Chirality : 0.044 0.261 2010 Planarity : 0.006 0.085 2410 Dihedral : 11.333 114.991 2249 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.08 % Allowed : 23.87 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1630 helix: 1.81 (0.75), residues: 50 sheet: -0.23 (0.19), residues: 650 loop : -1.04 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 133 HIS 0.004 0.001 HIS E 62 PHE 0.017 0.002 PHE C 2 TYR 0.013 0.002 TYR A 117 ARG 0.008 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 15) link_NAG-ASN : angle 2.38421 ( 45) link_BETA1-4 : bond 0.00913 ( 5) link_BETA1-4 : angle 5.19250 ( 15) hydrogen bonds : bond 0.03708 ( 421) hydrogen bonds : angle 5.47614 ( 1230) SS BOND : bond 0.00496 ( 16) SS BOND : angle 0.91717 ( 32) covalent geometry : bond 0.00626 (13805) covalent geometry : angle 0.65916 (18755) *********************** 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 310 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 1.437 Fit side-chains REVERT: A 97 GLU cc_start: 0.9062 (pt0) cc_final: 0.8685 (mp0) REVERT: A 191 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8147 (tmtt) REVERT: B 97 GLU cc_start: 0.9076 (pt0) cc_final: 0.8747 (mp0) REVERT: D 97 GLU cc_start: 0.9154 (pt0) cc_final: 0.8734 (mp0) REVERT: D 172 GLU cc_start: 0.8739 (tt0) cc_final: 0.8522 (tt0) REVERT: D 192 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: E 97 GLU cc_start: 0.9059 (pt0) cc_final: 0.8703 (mp0) REVERT: E 205 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (ttp-170) REVERT: H 73 ASP cc_start: 0.9077 (t0) cc_final: 0.8716 (t0) REVERT: I 45 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8270 (ttp80) REVERT: I 73 ASP cc_start: 0.8988 (t0) cc_final: 0.8696 (t0) REVERT: J 45 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8249 (tpp80) REVERT: J 51 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9237 (tp) REVERT: J 84 ASN cc_start: 0.8146 (m-40) cc_final: 0.7907 (m-40) outliers start: 58 outliers final: 24 residues processed: 294 average time/residue: 1.7703 time to fit residues: 553.0156 Evaluate side-chains 277 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 191 LYS 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 E residue 205 ARG 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 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 76 LYS 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 51 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.053235 restraints weight = 55336.490| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 3.67 r_work: 0.2418 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2412 r_free = 0.2412 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 = 0.2412 r_free = 0.2412 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13841 Z= 0.150 Angle : 0.633 8.211 18847 Z= 0.318 Chirality : 0.042 0.220 2010 Planarity : 0.005 0.074 2410 Dihedral : 10.834 115.599 2247 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.80 % Allowed : 24.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1630 helix: 2.90 (0.74), residues: 45 sheet: -0.21 (0.19), residues: 650 loop : -1.16 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 133 HIS 0.002 0.001 HIS E 62 PHE 0.011 0.001 PHE C 2 TYR 0.013 0.001 TYR B 117 ARG 0.010 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 15) link_NAG-ASN : angle 2.29499 ( 45) link_BETA1-4 : bond 0.01207 ( 5) link_BETA1-4 : angle 4.96804 ( 15) hydrogen bonds : bond 0.02990 ( 421) hydrogen bonds : angle 5.21838 ( 1230) SS BOND : bond 0.00355 ( 16) SS BOND : angle 0.74847 ( 32) covalent geometry : bond 0.00346 (13805) covalent geometry : angle 0.60771 (18755) *********************** 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 310 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9173 (mtmm) REVERT: A 97 GLU cc_start: 0.9065 (pt0) cc_final: 0.8717 (mp0) REVERT: A 191 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8166 (tmtt) REVERT: B 97 GLU cc_start: 0.9074 (pt0) cc_final: 0.8765 (mp0) REVERT: B 192 GLU cc_start: 0.8425 (tp30) cc_final: 0.8175 (tp30) REVERT: C 181 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9176 (ptmm) REVERT: D 46 ASN cc_start: 0.9353 (m110) cc_final: 0.9151 (m110) REVERT: D 97 GLU cc_start: 0.9166 (pt0) cc_final: 0.8771 (mp0) REVERT: D 192 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: E 97 GLU cc_start: 0.9070 (pt0) cc_final: 0.8731 (mp0) REVERT: E 205 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8415 (ttp-170) REVERT: H 73 ASP cc_start: 0.9070 (t0) cc_final: 0.8717 (t0) REVERT: I 73 ASP cc_start: 0.9003 (t0) cc_final: 0.8662 (t0) outliers start: 54 outliers final: 21 residues processed: 292 average time/residue: 1.7429 time to fit residues: 540.8626 Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain G residue 44 GLU 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 76 LYS 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 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 154 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 117 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN F 13 GLN G 13 GLN I 13 GLN J 13 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.055203 restraints weight = 57203.784| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.76 r_work: 0.2462 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 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 = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 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 : 0.003 0.040 13841 Z= 0.118 Angle : 0.618 8.100 18847 Z= 0.310 Chirality : 0.041 0.204 2010 Planarity : 0.005 0.069 2410 Dihedral : 10.352 115.120 2244 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.31 % Allowed : 25.35 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1630 helix: 2.87 (0.75), residues: 45 sheet: -0.18 (0.19), residues: 655 loop : -1.19 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 133 HIS 0.001 0.000 HIS E 62 PHE 0.008 0.001 PHE C 136 TYR 0.013 0.001 TYR C 117 ARG 0.010 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 15) link_NAG-ASN : angle 2.16142 ( 45) link_BETA1-4 : bond 0.01274 ( 5) link_BETA1-4 : angle 4.72810 ( 15) hydrogen bonds : bond 0.02627 ( 421) hydrogen bonds : angle 4.98833 ( 1230) SS BOND : bond 0.00332 ( 16) SS BOND : angle 0.67794 ( 32) covalent geometry : bond 0.00276 (13805) covalent geometry : angle 0.59451 (18755) *********************** 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 311 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9145 (mtmm) REVERT: A 97 GLU cc_start: 0.9069 (pt0) cc_final: 0.8685 (mp0) REVERT: A 191 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8181 (tmtt) REVERT: C 181 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9160 (ptmm) REVERT: C 192 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: D 46 ASN cc_start: 0.9344 (m110) cc_final: 0.9136 (m110) REVERT: D 97 GLU cc_start: 0.9161 (pt0) cc_final: 0.8729 (mp0) REVERT: D 192 GLU cc_start: 0.8420 (tp30) cc_final: 0.8149 (tp30) REVERT: E 97 GLU cc_start: 0.9107 (pt0) cc_final: 0.8722 (mp0) REVERT: E 170 ASN cc_start: 0.9099 (t0) cc_final: 0.8470 (t0) REVERT: F 43 LYS cc_start: 0.9277 (ttmm) cc_final: 0.9063 (mppt) REVERT: F 84 ASN cc_start: 0.7833 (m-40) cc_final: 0.7603 (m110) REVERT: G 84 ASN cc_start: 0.7505 (m110) cc_final: 0.7279 (m110) REVERT: G 121 THR cc_start: 0.9545 (m) cc_final: 0.9182 (p) REVERT: H 3 GLN cc_start: 0.8740 (mt0) cc_final: 0.8482 (tt0) REVERT: H 73 ASP cc_start: 0.9062 (t0) cc_final: 0.8739 (t0) REVERT: I 45 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7867 (tpp80) REVERT: I 73 ASP cc_start: 0.8994 (t0) cc_final: 0.8647 (t0) REVERT: I 87 LYS cc_start: 0.9270 (mttt) cc_final: 0.8993 (mttp) outliers start: 47 outliers final: 20 residues processed: 301 average time/residue: 1.8231 time to fit residues: 581.8842 Evaluate side-chains 273 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G 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 76 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN F 13 GLN G 13 GLN I 13 GLN J 13 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.072174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.051057 restraints weight = 51445.799| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 3.53 r_work: 0.2364 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2345 r_free = 0.2345 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 = 0.2345 r_free = 0.2345 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13841 Z= 0.302 Angle : 0.705 8.532 18847 Z= 0.353 Chirality : 0.045 0.214 2010 Planarity : 0.005 0.069 2410 Dihedral : 10.519 115.397 2242 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.17 % Allowed : 25.92 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1630 helix: 1.57 (0.76), residues: 50 sheet: -0.25 (0.19), residues: 650 loop : -1.16 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 133 HIS 0.005 0.001 HIS E 62 PHE 0.017 0.002 PHE D 2 TYR 0.011 0.002 TYR E 128 ARG 0.008 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 15) link_NAG-ASN : angle 2.34008 ( 45) link_BETA1-4 : bond 0.00833 ( 5) link_BETA1-4 : angle 5.05816 ( 15) hydrogen bonds : bond 0.03549 ( 421) hydrogen bonds : angle 5.30481 ( 1230) SS BOND : bond 0.00525 ( 16) SS BOND : angle 1.06910 ( 32) covalent geometry : bond 0.00696 (13805) covalent geometry : angle 0.68065 (18755) *********************** 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: 45 poor density : 245 time to evaluate : 1.599 Fit side-chains REVERT: A 75 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9204 (mtmm) REVERT: A 97 GLU cc_start: 0.9071 (pt0) cc_final: 0.8755 (mp0) REVERT: A 191 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8122 (tmtt) REVERT: C 75 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9111 (mtmm) REVERT: C 181 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9171 (ptmm) REVERT: D 46 ASN cc_start: 0.9374 (m-40) cc_final: 0.9168 (m110) REVERT: D 97 GLU cc_start: 0.9142 (pt0) cc_final: 0.8712 (mp0) REVERT: E 97 GLU cc_start: 0.9089 (pt0) cc_final: 0.8726 (mp0) REVERT: F 73 ASP cc_start: 0.9096 (t0) cc_final: 0.8865 (t0) REVERT: H 3 GLN cc_start: 0.8827 (mt0) cc_final: 0.8565 (tt0) REVERT: H 73 ASP cc_start: 0.9091 (t0) cc_final: 0.8595 (t0) REVERT: I 45 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7980 (tpp80) REVERT: I 73 ASP cc_start: 0.9040 (t0) cc_final: 0.8649 (t0) REVERT: I 87 LYS cc_start: 0.9331 (mttt) cc_final: 0.9119 (mttp) REVERT: J 84 ASN cc_start: 0.8232 (m-40) cc_final: 0.8005 (m-40) REVERT: J 108 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8290 (mtt180) outliers start: 45 outliers final: 23 residues processed: 279 average time/residue: 1.8157 time to fit residues: 540.8237 Evaluate side-chains 272 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 75 LYS 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 F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 76 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.051555 restraints weight = 71354.178| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 3.99 r_work: 0.2379 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 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 = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2022 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= 0.183 Angle : 0.661 8.040 18847 Z= 0.332 Chirality : 0.042 0.196 2010 Planarity : 0.005 0.066 2410 Dihedral : 10.400 115.381 2242 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.46 % Allowed : 26.48 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1630 helix: 1.54 (0.76), residues: 50 sheet: -0.31 (0.19), residues: 650 loop : -1.15 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 133 HIS 0.002 0.001 HIS A 62 PHE 0.012 0.001 PHE E 2 TYR 0.010 0.001 TYR B 117 ARG 0.009 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 15) link_NAG-ASN : angle 2.26855 ( 45) link_BETA1-4 : bond 0.01070 ( 5) link_BETA1-4 : angle 4.90017 ( 15) hydrogen bonds : bond 0.03057 ( 421) hydrogen bonds : angle 5.20391 ( 1230) SS BOND : bond 0.00386 ( 16) SS BOND : angle 1.01294 ( 32) covalent geometry : bond 0.00422 (13805) covalent geometry : angle 0.63721 (18755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 1.476 Fit side-chains REVERT: A 75 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9194 (mtmm) REVERT: A 97 GLU cc_start: 0.9062 (pt0) cc_final: 0.8722 (mp0) REVERT: A 191 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8136 (tmtt) REVERT: C 181 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9171 (ptmm) REVERT: D 97 GLU cc_start: 0.9152 (pt0) cc_final: 0.8704 (mp0) REVERT: E 97 GLU cc_start: 0.9090 (pt0) cc_final: 0.8722 (mp0) REVERT: H 3 GLN cc_start: 0.8820 (mt0) cc_final: 0.8551 (tt0) REVERT: H 73 ASP cc_start: 0.9053 (t0) cc_final: 0.8830 (t0) REVERT: I 45 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7994 (tpp80) REVERT: I 73 ASP cc_start: 0.9038 (t0) cc_final: 0.8629 (t0) REVERT: J 108 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8292 (mtt180) outliers start: 35 outliers final: 23 residues processed: 276 average time/residue: 1.7456 time to fit residues: 512.5551 Evaluate side-chains 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 2.058 ------------------------------------------------------------------------------- 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 176 VAL 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 F residue 65 LYS 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 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 65 LYS 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 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 13 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 146 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 121 optimal weight: 0.1980 chunk 122 optimal weight: 5.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN G 84 ASN I 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.076791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.055405 restraints weight = 67056.707| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 3.97 r_work: 0.2457 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2443 r_free = 0.2443 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 = 0.2443 r_free = 0.2443 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13841 Z= 0.118 Angle : 0.635 8.023 18847 Z= 0.320 Chirality : 0.041 0.178 2010 Planarity : 0.005 0.062 2410 Dihedral : 10.069 115.056 2242 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.25 % Allowed : 27.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1630 helix: 2.59 (0.76), residues: 45 sheet: -0.17 (0.19), residues: 650 loop : -1.21 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 133 HIS 0.001 0.000 HIS E 62 PHE 0.008 0.001 PHE D 136 TYR 0.016 0.001 TYR D 128 ARG 0.010 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 2.08183 ( 45) link_BETA1-4 : bond 0.01188 ( 5) link_BETA1-4 : angle 4.59317 ( 15) hydrogen bonds : bond 0.02519 ( 421) hydrogen bonds : angle 4.94180 ( 1230) SS BOND : bond 0.00307 ( 16) SS BOND : angle 0.81376 ( 32) covalent geometry : bond 0.00277 (13805) covalent geometry : angle 0.61398 (18755) *********************** 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 284 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 1.400 Fit side-chains REVERT: A 97 GLU cc_start: 0.9072 (pt0) cc_final: 0.8669 (mp0) REVERT: A 191 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8130 (tmtt) REVERT: A 205 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8212 (ttp-170) REVERT: C 181 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9147 (ptmm) REVERT: D 9 GLU cc_start: 0.8984 (tp30) cc_final: 0.8778 (tp30) REVERT: D 97 GLU cc_start: 0.9144 (pt0) cc_final: 0.8689 (mp0) REVERT: D 192 GLU cc_start: 0.8561 (tp30) cc_final: 0.8220 (tp30) REVERT: E 97 GLU cc_start: 0.9081 (pt0) cc_final: 0.8696 (mp0) REVERT: F 43 LYS cc_start: 0.9300 (ttmm) cc_final: 0.9052 (mppt) REVERT: F 87 LYS cc_start: 0.9324 (mttt) cc_final: 0.9081 (ptpt) REVERT: G 73 ASP cc_start: 0.8973 (t0) cc_final: 0.8716 (t0) REVERT: H 3 GLN cc_start: 0.8793 (mt0) cc_final: 0.8513 (tt0) REVERT: I 45 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8055 (tpp80) REVERT: I 73 ASP cc_start: 0.9028 (t0) cc_final: 0.8621 (t0) REVERT: J 44 GLU cc_start: 0.8620 (tp30) cc_final: 0.8382 (tp30) REVERT: J 73 ASP cc_start: 0.8989 (t0) cc_final: 0.8703 (t0) outliers start: 32 outliers final: 20 residues processed: 279 average time/residue: 1.7552 time to fit residues: 520.4211 Evaluate side-chains 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain 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 76 LYS 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 H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 65 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN I 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.052792 restraints weight = 67516.317| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.95 r_work: 0.2396 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2380 r_free = 0.2380 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2380 r_free = 0.2380 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.2187 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= 0.183 Angle : 0.658 7.658 18847 Z= 0.331 Chirality : 0.042 0.194 2010 Planarity : 0.005 0.062 2410 Dihedral : 10.170 115.082 2242 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 1630 helix: 1.48 (0.77), residues: 50 sheet: -0.19 (0.19), residues: 645 loop : -1.18 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP E 133 HIS 0.002 0.001 HIS E 62 PHE 0.012 0.001 PHE D 2 TYR 0.009 0.001 TYR C 117 ARG 0.009 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 15) link_NAG-ASN : angle 2.10019 ( 45) link_BETA1-4 : bond 0.01110 ( 5) link_BETA1-4 : angle 4.71433 ( 15) hydrogen bonds : bond 0.02981 ( 421) hydrogen bonds : angle 5.03463 ( 1230) SS BOND : bond 0.00346 ( 16) SS BOND : angle 0.93270 ( 32) covalent geometry : bond 0.00430 (13805) covalent geometry : angle 0.63662 (18755) *********************** 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 278 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 1.490 Fit side-chains REVERT: A 97 GLU cc_start: 0.9076 (pt0) cc_final: 0.8709 (mp0) REVERT: A 191 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8121 (tmtt) REVERT: C 181 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9165 (ptmm) REVERT: E 97 GLU cc_start: 0.9088 (pt0) cc_final: 0.8705 (mp0) REVERT: F 43 LYS cc_start: 0.9324 (ttmm) cc_final: 0.9062 (mppt) REVERT: F 73 ASP cc_start: 0.9104 (t0) cc_final: 0.8663 (t0) REVERT: F 87 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9131 (ptpt) REVERT: G 73 ASP cc_start: 0.9012 (t0) cc_final: 0.8624 (t0) REVERT: H 3 GLN cc_start: 0.8837 (mt0) cc_final: 0.8551 (tt0) REVERT: I 45 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8137 (tpp80) REVERT: I 73 ASP cc_start: 0.9058 (t0) cc_final: 0.8657 (t0) REVERT: J 44 GLU cc_start: 0.8658 (tp30) cc_final: 0.8450 (tp30) REVERT: J 73 ASP cc_start: 0.9046 (t0) cc_final: 0.8737 (t0) outliers start: 29 outliers final: 19 residues processed: 271 average time/residue: 1.7600 time to fit residues: 507.1858 Evaluate side-chains 264 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.073809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.052671 restraints weight = 55354.554| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.66 r_work: 0.2402 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 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 = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2221 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= 0.186 Angle : 0.672 7.843 18847 Z= 0.338 Chirality : 0.042 0.192 2010 Planarity : 0.005 0.062 2410 Dihedral : 10.204 115.134 2242 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 1630 helix: 1.40 (0.76), residues: 50 sheet: -0.21 (0.19), residues: 645 loop : -1.14 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 133 HIS 0.002 0.001 HIS A 62 PHE 0.012 0.001 PHE D 2 TYR 0.016 0.001 TYR E 128 ARG 0.009 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 15) link_NAG-ASN : angle 2.13006 ( 45) link_BETA1-4 : bond 0.01067 ( 5) link_BETA1-4 : angle 4.75643 ( 15) hydrogen bonds : bond 0.03017 ( 421) hydrogen bonds : angle 5.08795 ( 1230) SS BOND : bond 0.00338 ( 16) SS BOND : angle 0.93259 ( 32) covalent geometry : bond 0.00435 (13805) covalent geometry : angle 0.65026 (18755) ********************** 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 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 1.486 Fit side-chains REVERT: A 97 GLU cc_start: 0.9049 (pt0) cc_final: 0.8694 (mp0) REVERT: A 191 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8096 (tmtt) REVERT: C 181 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9172 (ptmm) REVERT: D 205 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.7838 (ttp-170) REVERT: E 97 GLU cc_start: 0.9068 (pt0) cc_final: 0.8697 (mp0) REVERT: F 73 ASP cc_start: 0.9075 (t0) cc_final: 0.8646 (t0) REVERT: G 73 ASP cc_start: 0.8967 (t0) cc_final: 0.8675 (t0) REVERT: H 3 GLN cc_start: 0.8838 (mt0) cc_final: 0.8553 (tt0) REVERT: H 73 ASP cc_start: 0.8892 (t0) cc_final: 0.8679 (t0) REVERT: I 45 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8093 (tpp80) REVERT: I 73 ASP cc_start: 0.9045 (t0) cc_final: 0.8628 (t0) REVERT: J 19 ARG cc_start: 0.8708 (tpp80) cc_final: 0.8473 (ttt-90) REVERT: J 44 GLU cc_start: 0.8689 (tp30) cc_final: 0.8484 (tp30) REVERT: J 73 ASP cc_start: 0.9019 (t0) cc_final: 0.8699 (t0) outliers start: 27 outliers final: 21 residues processed: 266 average time/residue: 1.7869 time to fit residues: 505.4732 Evaluate side-chains 263 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 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 155 optimal weight: 0.0570 chunk 125 optimal weight: 7.9990 chunk 104 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 113 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.054691 restraints weight = 63682.392| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 3.91 r_work: 0.2447 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13841 Z= 0.123 Angle : 0.633 7.852 18847 Z= 0.320 Chirality : 0.041 0.184 2010 Planarity : 0.005 0.061 2410 Dihedral : 10.030 114.705 2242 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.90 % Allowed : 28.10 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1630 helix: 2.21 (0.76), residues: 45 sheet: -0.14 (0.19), residues: 645 loop : -1.18 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 133 HIS 0.001 0.000 HIS E 62 PHE 0.008 0.001 PHE D 2 TYR 0.012 0.001 TYR C 117 ARG 0.009 0.001 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 15) link_NAG-ASN : angle 1.96548 ( 45) link_BETA1-4 : bond 0.01256 ( 5) link_BETA1-4 : angle 4.57523 ( 15) hydrogen bonds : bond 0.02597 ( 421) hydrogen bonds : angle 4.90739 ( 1230) SS BOND : bond 0.00280 ( 16) SS BOND : angle 0.78326 ( 32) covalent geometry : bond 0.00293 (13805) covalent geometry : angle 0.61337 (18755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11553.29 seconds wall clock time: 199 minutes 7.54 seconds (11947.54 seconds total)