Starting phenix.real_space_refine on Mon May 19 01:54:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tx3_41676/05_2025/8tx3_41676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tx3_41676/05_2025/8tx3_41676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tx3_41676/05_2025/8tx3_41676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tx3_41676/05_2025/8tx3_41676.map" model { file = "/net/cci-nas-00/data/ceres_data/8tx3_41676/05_2025/8tx3_41676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tx3_41676/05_2025/8tx3_41676.cif" } resolution = 2.99 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= 0.094 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 81 5.16 5 C 11182 2.51 5 N 2975 2.21 5 O 3685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17923 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2545 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1393 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2545 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1393 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "G" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2545 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "I" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1393 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "E" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "F" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.22, per 1000 atoms: 0.57 Number of scatterers: 17923 At special positions: 0 Unit cell: (140.27, 130.31, 150.23, 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 81 16.00 O 3685 8.00 N 2975 7.00 C 11182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.39 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS I 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS G 30 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.02 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 402 " - " ASN A 63 " " NAG A 403 " - " ASN A 126 " " NAG A 404 " - " ASN A 133 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 63 " " NAG C 403 " - " ASN C 126 " " NAG C 404 " - " ASN C 133 " " NAG D 301 " - " ASN D 154 " " NAG G 401 " - " ASN G 22 " " NAG G 402 " - " ASN G 63 " " NAG G 403 " - " ASN G 126 " " NAG G 404 " - " ASN G 133 " " NAG R 1 " - " ASN C 165 " " NAG S 1 " - " ASN C 246 " " NAG T 1 " - " ASN C 285 " Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 2.0 seconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 50 sheets defined 18.6% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.805A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 38 through 56 Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.569A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.572A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.754A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.741A pdb=" N LEU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 127 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.643A pdb=" N ARG D 153 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.533A pdb=" N ASP G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLY G 78 " --> pdb=" O GLN G 75 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN G 80 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 116 Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 38 through 56 Processing helix chain 'I' and resid 75 through 127 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.645A pdb=" N TRP H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.717A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.661A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.590A pdb=" N SER E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.878A pdb=" N ILE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.533A pdb=" N SER F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.557A pdb=" N ILE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 37 removed outlier: 3.611A pdb=" N GLY B 31 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.182A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 removed outlier: 7.779A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.510A pdb=" N LEU A 243 " --> pdb=" O MET A 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 37 removed outlier: 4.745A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 12 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.419A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.710A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.585A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.585A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.482A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.597A pdb=" N LEU C 243 " --> pdb=" O MET C 168 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 303 through 305 removed outlier: 3.655A pdb=" N CYS C 305 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN D 60 " --> pdb=" O CYS C 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 31 through 37 removed outlier: 3.705A pdb=" N ASN I 28 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR I 22 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY I 23 " --> pdb=" O GLY G 16 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN I 27 " --> pdb=" O THR G 12 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR G 12 " --> pdb=" O GLN I 27 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'G' and resid 51 through 52 removed outlier: 6.972A pdb=" N ILE G 51 " --> pdb=" O GLY G 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 58 through 60 Processing sheet with id=AD3, first strand: chain 'G' and resid 121 through 122 Processing sheet with id=AD4, first strand: chain 'G' and resid 136 through 140 removed outlier: 4.657A pdb=" N CYS G 139 " --> pdb=" O SER G 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 151 through 153 removed outlier: 7.847A pdb=" N ILE G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 229 " --> pdb=" O HIS G 184 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 164 through 169 removed outlier: 3.516A pdb=" N ILE G 245 " --> pdb=" O VAL G 166 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 281 through 282 removed outlier: 4.427A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 288 " --> pdb=" O CYS G 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 303 through 304 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.519A pdb=" N THR H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.562A pdb=" N TYR H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 58 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.562A pdb=" N TYR H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 58 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.527A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.884A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'E' and resid 56 through 59 removed outlier: 3.603A pdb=" N TYR E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER E 58 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 56 through 59 removed outlier: 3.603A pdb=" N TYR E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER E 58 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 4 through 6 removed outlier: 6.124A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 11.167A pdb=" N GLN J 27 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N SER J 67 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 11.813A pdb=" N ILE J 29 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 11.732A pdb=" N SER J 65 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.674A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.585A pdb=" N TYR F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER F 58 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.585A pdb=" N TYR F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER F 58 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.947A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.800A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2914 1.30 - 1.43: 4941 1.43 - 1.56: 10332 1.56 - 1.69: 3 1.69 - 1.83: 108 Bond restraints: 18298 Sorted by residual: bond pdb=" CA SER K 91 " pdb=" CB SER K 91 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.02e-02 9.61e+03 2.77e+01 bond pdb=" CA SER K 92 " pdb=" CB SER K 92 " ideal model delta sigma weight residual 1.536 1.451 0.085 1.65e-02 3.67e+03 2.63e+01 bond pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CA ALA C 19 " pdb=" CB ALA C 19 " ideal model delta sigma weight residual 1.534 1.466 0.067 1.57e-02 4.06e+03 1.83e+01 bond pdb=" CA SER B 71 " pdb=" CB SER B 71 " ideal model delta sigma weight residual 1.532 1.472 0.060 1.53e-02 4.27e+03 1.56e+01 ... (remaining 18293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 23928 2.15 - 4.30: 686 4.30 - 6.45: 163 6.45 - 8.60: 24 8.60 - 10.75: 5 Bond angle restraints: 24806 Sorted by residual: angle pdb=" CA PHE D 9 " pdb=" CB PHE D 9 " pdb=" CG PHE D 9 " ideal model delta sigma weight residual 113.80 122.14 -8.34 1.00e+00 1.00e+00 6.95e+01 angle pdb=" C SER K 92 " pdb=" N LYS K 93 " pdb=" CA LYS K 93 " ideal model delta sigma weight residual 122.74 111.99 10.75 1.54e+00 4.22e-01 4.87e+01 angle pdb=" C CYS C 30 " pdb=" CA CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sigma weight residual 110.86 101.30 9.56 1.65e+00 3.67e-01 3.35e+01 angle pdb=" N LEU B 80 " pdb=" CA LEU B 80 " pdb=" C LEU B 80 " ideal model delta sigma weight residual 111.69 105.00 6.69 1.23e+00 6.61e-01 2.96e+01 angle pdb=" C CYS A 14 " pdb=" CA CYS A 14 " pdb=" CB CYS A 14 " ideal model delta sigma weight residual 110.36 101.04 9.32 1.78e+00 3.16e-01 2.74e+01 ... (remaining 24801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 10988 23.96 - 47.93: 570 47.93 - 71.89: 101 71.89 - 95.86: 90 95.86 - 119.82: 71 Dihedral angle restraints: 11820 sinusoidal: 5556 harmonic: 6264 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 172.76 -79.76 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 161.06 -68.06 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS I 144 " pdb=" SG CYS I 144 " pdb=" SG CYS I 148 " pdb=" CB CYS I 148 " ideal model delta sinusoidal sigma weight residual 93.00 157.39 -64.39 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 11817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 2853 0.172 - 0.343: 35 0.343 - 0.515: 0 0.515 - 0.687: 0 0.687 - 0.858: 1 Chirality restraints: 2889 Sorted by residual: chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 22 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" CB VAL B 73 " pdb=" CA VAL B 73 " pdb=" CG1 VAL B 73 " pdb=" CG2 VAL B 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE J 83 " pdb=" CA ILE J 83 " pdb=" CG1 ILE J 83 " pdb=" CG2 ILE J 83 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2886 not shown) Planarity restraints: 3126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER K 92 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C SER K 92 " 0.054 2.00e-02 2.50e+03 pdb=" O SER K 92 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS K 93 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 18 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C HIS C 18 " -0.048 2.00e-02 2.50e+03 pdb=" O HIS C 18 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 19 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 73 " -0.045 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO G 74 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " -0.038 5.00e-02 4.00e+02 ... (remaining 3123 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 368 2.68 - 3.23: 15631 3.23 - 3.79: 27863 3.79 - 4.34: 38830 4.34 - 4.90: 64393 Nonbonded interactions: 147085 Sorted by model distance: nonbonded pdb=" NE ARG I 25 " pdb=" NE2 GLN I 34 " model vdw 2.121 3.200 nonbonded pdb=" OG1 THR G 283 " pdb=" O GLY G 286 " model vdw 2.241 3.040 nonbonded pdb=" OG SER D 113 " pdb=" O ILE I 2 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 98 " pdb=" OG SER A 228 " model vdw 2.281 3.040 nonbonded pdb=" O PRO C 4 " pdb=" NE2 GLN D 27 " model vdw 2.285 3.120 ... (remaining 147080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 1 through 173) selection = (chain 'D' and resid 1 through 173) selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 38.470 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.006 0.358 18382 Z= 0.331 Angle : 0.913 28.942 25032 Z= 0.484 Chirality : 0.059 0.858 2889 Planarity : 0.005 0.069 3110 Dihedral : 18.841 119.820 7740 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.26 % Allowed : 0.47 % Favored : 99.26 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.45 % 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: -1.17 (0.17), residues: 2148 helix: 0.82 (0.25), residues: 357 sheet: -0.95 (0.23), residues: 564 loop : -1.16 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 96 HIS 0.005 0.001 HIS I 106 PHE 0.043 0.002 PHE D 9 TYR 0.027 0.001 TYR E 100 ARG 0.010 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 16) link_NAG-ASN : angle 3.95928 ( 48) link_ALPHA1-6 : bond 0.00488 ( 9) link_ALPHA1-6 : angle 1.39376 ( 27) link_BETA1-4 : bond 0.00663 ( 24) link_BETA1-4 : angle 1.70030 ( 72) link_ALPHA1-3 : bond 0.00750 ( 9) link_ALPHA1-3 : angle 2.03016 ( 27) hydrogen bonds : bond 0.19465 ( 625) hydrogen bonds : angle 8.42629 ( 1761) SS BOND : bond 0.07032 ( 26) SS BOND : angle 4.40937 ( 52) covalent geometry : bond 0.00535 (18298) covalent geometry : angle 0.86856 (24806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 290 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.6765 (m-40) cc_final: 0.6564 (t0) REVERT: D 37 ASP cc_start: 0.8241 (t70) cc_final: 0.7858 (t70) REVERT: I 79 ASP cc_start: 0.8122 (m-30) cc_final: 0.7915 (m-30) REVERT: E 13 MET cc_start: 0.6898 (mmt) cc_final: 0.6001 (ptt) outliers start: 5 outliers final: 1 residues processed: 293 average time/residue: 0.9956 time to fit residues: 335.0606 Evaluate side-chains 228 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 53 ASN B 168 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 60 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 105 GLN L 34 ASN L 90 GLN E 6 GLN K 34 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114064 restraints weight = 21444.567| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.21 r_work: 0.3178 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 18382 Z= 0.253 Angle : 0.763 14.633 25032 Z= 0.368 Chirality : 0.051 0.417 2889 Planarity : 0.005 0.052 3110 Dihedral : 15.457 99.390 3720 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 2.00 % Allowed : 9.55 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.18), residues: 2148 helix: 1.36 (0.26), residues: 353 sheet: -1.19 (0.20), residues: 615 loop : -0.97 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 96 HIS 0.011 0.002 HIS I 159 PHE 0.020 0.002 PHE D 9 TYR 0.023 0.002 TYR J 49 ARG 0.005 0.001 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 16) link_NAG-ASN : angle 3.88513 ( 48) link_ALPHA1-6 : bond 0.00832 ( 9) link_ALPHA1-6 : angle 1.82869 ( 27) link_BETA1-4 : bond 0.00563 ( 24) link_BETA1-4 : angle 2.30999 ( 72) link_ALPHA1-3 : bond 0.01093 ( 9) link_ALPHA1-3 : angle 2.53652 ( 27) hydrogen bonds : bond 0.04447 ( 625) hydrogen bonds : angle 5.73191 ( 1761) SS BOND : bond 0.00428 ( 26) SS BOND : angle 1.81926 ( 52) covalent geometry : bond 0.00605 (18298) covalent geometry : angle 0.72462 (24806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7124 (m-40) cc_final: 0.6577 (OUTLIER) REVERT: A 75 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7776 (pp30) REVERT: C 144 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.6928 (m110) REVERT: C 201 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7643 (ttp-110) REVERT: D 27 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: G 144 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7113 (m110) REVERT: G 156 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: G 188 ASP cc_start: 0.7846 (t0) cc_final: 0.7252 (m-30) REVERT: G 321 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7699 (ttt180) REVERT: I 79 ASP cc_start: 0.8423 (m-30) cc_final: 0.8187 (m-30) REVERT: I 170 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.5759 (mmt180) REVERT: E 56 TYR cc_start: 0.8806 (t80) cc_final: 0.8587 (t80) REVERT: E 86 ASP cc_start: 0.7959 (m-30) cc_final: 0.7756 (m-30) REVERT: F 17 SER cc_start: 0.8002 (p) cc_final: 0.7654 (m) outliers start: 38 outliers final: 14 residues processed: 249 average time/residue: 1.1456 time to fit residues: 324.0837 Evaluate side-chains 233 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 156 GLN Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 321 ARG Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 206 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 17 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN I 60 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121220 restraints weight = 21220.888| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.98 r_work: 0.3309 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 18382 Z= 0.211 Angle : 0.669 12.037 25032 Z= 0.326 Chirality : 0.048 0.468 2889 Planarity : 0.004 0.048 3110 Dihedral : 13.382 110.987 3717 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.43 % Allowed : 11.81 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.87 (0.18), residues: 2148 helix: 1.61 (0.27), residues: 356 sheet: -1.17 (0.20), residues: 609 loop : -0.90 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.010 0.002 HIS I 159 PHE 0.016 0.001 PHE D 9 TYR 0.021 0.001 TYR L 49 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 16) link_NAG-ASN : angle 3.28429 ( 48) link_ALPHA1-6 : bond 0.00955 ( 9) link_ALPHA1-6 : angle 1.73105 ( 27) link_BETA1-4 : bond 0.00536 ( 24) link_BETA1-4 : angle 1.98667 ( 72) link_ALPHA1-3 : bond 0.01442 ( 9) link_ALPHA1-3 : angle 2.28654 ( 27) hydrogen bonds : bond 0.04081 ( 625) hydrogen bonds : angle 5.33846 ( 1761) SS BOND : bond 0.00449 ( 26) SS BOND : angle 1.44498 ( 52) covalent geometry : bond 0.00499 (18298) covalent geometry : angle 0.63753 (24806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.7138 (m-40) cc_final: 0.6669 (t0) REVERT: B 61 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8063 (mp0) REVERT: C 144 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.6954 (m110) REVERT: C 201 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7661 (ttp-110) REVERT: D 37 ASP cc_start: 0.8574 (t70) cc_final: 0.8215 (t70) REVERT: G 144 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7199 (m110) REVERT: G 156 GLN cc_start: 0.8346 (pm20) cc_final: 0.8067 (pp30) REVERT: G 321 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7652 (ttt180) REVERT: I 79 ASP cc_start: 0.8455 (m-30) cc_final: 0.8231 (m-30) REVERT: I 170 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.5854 (mmt180) REVERT: H 30 ILE cc_start: 0.8830 (pt) cc_final: 0.8594 (mp) REVERT: E 56 TYR cc_start: 0.8960 (t80) cc_final: 0.8668 (t80) REVERT: E 86 ASP cc_start: 0.8332 (m-30) cc_final: 0.8084 (m-30) outliers start: 46 outliers final: 18 residues processed: 256 average time/residue: 1.1265 time to fit residues: 327.9117 Evaluate side-chains 234 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 321 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 201 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.0570 chunk 199 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 176 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 285 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 34 ASN K 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125984 restraints weight = 21104.451| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.03 r_work: 0.3410 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 18382 Z= 0.113 Angle : 0.597 11.615 25032 Z= 0.290 Chirality : 0.045 0.393 2889 Planarity : 0.004 0.046 3110 Dihedral : 11.589 103.229 3717 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.16 % Allowed : 13.50 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.65 (0.18), residues: 2148 helix: 1.98 (0.27), residues: 354 sheet: -1.03 (0.20), residues: 609 loop : -0.81 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.008 0.001 HIS I 159 PHE 0.015 0.001 PHE D 9 TYR 0.020 0.001 TYR L 49 ARG 0.006 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 16) link_NAG-ASN : angle 3.03659 ( 48) link_ALPHA1-6 : bond 0.00964 ( 9) link_ALPHA1-6 : angle 1.86742 ( 27) link_BETA1-4 : bond 0.00441 ( 24) link_BETA1-4 : angle 1.91631 ( 72) link_ALPHA1-3 : bond 0.01579 ( 9) link_ALPHA1-3 : angle 2.45804 ( 27) hydrogen bonds : bond 0.03387 ( 625) hydrogen bonds : angle 4.97451 ( 1761) SS BOND : bond 0.00356 ( 26) SS BOND : angle 1.89280 ( 52) covalent geometry : bond 0.00241 (18298) covalent geometry : angle 0.56010 (24806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.6962 (m-40) cc_final: 0.6532 (t0) REVERT: C 77 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: C 201 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7581 (ttp-110) REVERT: G 156 GLN cc_start: 0.8397 (pm20) cc_final: 0.8082 (pp30) REVERT: I 79 ASP cc_start: 0.8446 (m-30) cc_final: 0.8204 (m-30) REVERT: I 153 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.5766 (mpp80) REVERT: E 13 MET cc_start: 0.7147 (mmt) cc_final: 0.5944 (ptt) REVERT: E 56 TYR cc_start: 0.8975 (t80) cc_final: 0.8699 (t80) REVERT: E 86 ASP cc_start: 0.8386 (m-30) cc_final: 0.8148 (m-30) outliers start: 41 outliers final: 15 residues processed: 262 average time/residue: 1.0541 time to fit residues: 314.5810 Evaluate side-chains 226 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 34 ASN F 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116154 restraints weight = 21674.725| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.10 r_work: 0.3244 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 18382 Z= 0.324 Angle : 0.758 11.109 25032 Z= 0.373 Chirality : 0.051 0.401 2889 Planarity : 0.005 0.054 3110 Dihedral : 11.242 104.799 3717 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.06 % Allowed : 14.72 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2148 helix: 1.39 (0.26), residues: 360 sheet: -1.25 (0.20), residues: 597 loop : -0.93 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 96 HIS 0.010 0.002 HIS I 159 PHE 0.015 0.002 PHE A 120 TYR 0.022 0.002 TYR L 49 ARG 0.005 0.001 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 16) link_NAG-ASN : angle 3.33939 ( 48) link_ALPHA1-6 : bond 0.01040 ( 9) link_ALPHA1-6 : angle 1.86078 ( 27) link_BETA1-4 : bond 0.00582 ( 24) link_BETA1-4 : angle 2.11015 ( 72) link_ALPHA1-3 : bond 0.01537 ( 9) link_ALPHA1-3 : angle 2.36556 ( 27) hydrogen bonds : bond 0.04361 ( 625) hydrogen bonds : angle 5.28922 ( 1761) SS BOND : bond 0.00683 ( 26) SS BOND : angle 2.55317 ( 52) covalent geometry : bond 0.00781 (18298) covalent geometry : angle 0.72213 (24806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 201 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7747 (ttp-110) REVERT: G 53 ASP cc_start: 0.8553 (p0) cc_final: 0.8325 (p0) REVERT: G 156 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8092 (pp30) REVERT: G 188 ASP cc_start: 0.7921 (t0) cc_final: 0.7413 (m-30) REVERT: G 276 LYS cc_start: 0.8765 (mptp) cc_final: 0.8375 (mppt) REVERT: I 54 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7557 (mtt90) REVERT: I 153 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.5974 (mpp80) REVERT: I 170 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6171 (mmt180) REVERT: E 56 TYR cc_start: 0.8948 (t80) cc_final: 0.8705 (t80) REVERT: E 86 ASP cc_start: 0.8423 (m-30) cc_final: 0.8144 (m-30) REVERT: F 99 ASN cc_start: 0.9080 (p0) cc_final: 0.8822 (p0) REVERT: K 27 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7490 (pm20) outliers start: 58 outliers final: 29 residues processed: 244 average time/residue: 1.1596 time to fit residues: 322.2330 Evaluate side-chains 232 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 156 GLN Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 170 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 34 ASN K 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122243 restraints weight = 21367.225| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.04 r_work: 0.3355 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18382 Z= 0.143 Angle : 0.612 10.353 25032 Z= 0.299 Chirality : 0.046 0.346 2889 Planarity : 0.004 0.049 3110 Dihedral : 10.208 105.555 3717 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.06 % Allowed : 16.03 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.18), residues: 2148 helix: 1.68 (0.27), residues: 360 sheet: -1.15 (0.20), residues: 609 loop : -0.88 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 96 HIS 0.009 0.001 HIS A 18 PHE 0.019 0.001 PHE F 63 TYR 0.021 0.001 TYR L 49 ARG 0.004 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 16) link_NAG-ASN : angle 2.97568 ( 48) link_ALPHA1-6 : bond 0.01070 ( 9) link_ALPHA1-6 : angle 1.78889 ( 27) link_BETA1-4 : bond 0.00402 ( 24) link_BETA1-4 : angle 1.87396 ( 72) link_ALPHA1-3 : bond 0.01381 ( 9) link_ALPHA1-3 : angle 2.46899 ( 27) hydrogen bonds : bond 0.03550 ( 625) hydrogen bonds : angle 4.99272 ( 1761) SS BOND : bond 0.00513 ( 26) SS BOND : angle 1.95562 ( 52) covalent geometry : bond 0.00328 (18298) covalent geometry : angle 0.57708 (24806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: C 201 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7604 (ttp-110) REVERT: D 37 ASP cc_start: 0.8550 (t70) cc_final: 0.8185 (t70) REVERT: G 53 ASP cc_start: 0.8305 (p0) cc_final: 0.8077 (p0) REVERT: G 156 GLN cc_start: 0.8477 (pm20) cc_final: 0.8124 (pp30) REVERT: G 276 LYS cc_start: 0.8719 (mptp) cc_final: 0.8385 (mppt) REVERT: I 22 TYR cc_start: 0.9346 (m-80) cc_final: 0.8975 (m-80) REVERT: E 13 MET cc_start: 0.7186 (mmt) cc_final: 0.6028 (ptt) REVERT: E 56 TYR cc_start: 0.8976 (t80) cc_final: 0.8689 (t80) REVERT: E 86 ASP cc_start: 0.8503 (m-30) cc_final: 0.8227 (m-30) outliers start: 39 outliers final: 20 residues processed: 253 average time/residue: 1.0852 time to fit residues: 313.4874 Evaluate side-chains 230 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain K residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 186 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 145 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 28 ASN B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 ASN I 34 GLN I 53 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 34 ASN F 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123864 restraints weight = 21137.988| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.02 r_work: 0.3376 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18382 Z= 0.127 Angle : 0.591 10.001 25032 Z= 0.289 Chirality : 0.045 0.351 2889 Planarity : 0.004 0.043 3110 Dihedral : 9.201 104.945 3717 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.16 % Allowed : 16.77 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.69 (0.18), residues: 2148 helix: 1.89 (0.27), residues: 359 sheet: -1.05 (0.20), residues: 585 loop : -0.84 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 96 HIS 0.011 0.001 HIS A 18 PHE 0.017 0.001 PHE F 63 TYR 0.020 0.001 TYR L 49 ARG 0.008 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 16) link_NAG-ASN : angle 2.79973 ( 48) link_ALPHA1-6 : bond 0.01059 ( 9) link_ALPHA1-6 : angle 1.81251 ( 27) link_BETA1-4 : bond 0.00447 ( 24) link_BETA1-4 : angle 1.79080 ( 72) link_ALPHA1-3 : bond 0.01276 ( 9) link_ALPHA1-3 : angle 2.29937 ( 27) hydrogen bonds : bond 0.03413 ( 625) hydrogen bonds : angle 4.80924 ( 1761) SS BOND : bond 0.00442 ( 26) SS BOND : angle 1.88789 ( 52) covalent geometry : bond 0.00291 (18298) covalent geometry : angle 0.55750 (24806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 201 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7577 (ttp-110) REVERT: G 77 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: G 156 GLN cc_start: 0.8485 (pm20) cc_final: 0.8127 (pp30) REVERT: G 276 LYS cc_start: 0.8721 (mptp) cc_final: 0.8409 (mppt) REVERT: I 22 TYR cc_start: 0.9349 (m-80) cc_final: 0.8912 (m-80) REVERT: I 170 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6001 (mmt180) REVERT: E 13 MET cc_start: 0.7178 (mmt) cc_final: 0.6025 (ptt) REVERT: E 56 TYR cc_start: 0.8942 (t80) cc_final: 0.8691 (t80) REVERT: E 86 ASP cc_start: 0.8513 (m-30) cc_final: 0.8224 (m-30) REVERT: F 13 MET cc_start: 0.7163 (mmt) cc_final: 0.6106 (ptt) REVERT: K 27 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7519 (pm20) outliers start: 41 outliers final: 24 residues processed: 253 average time/residue: 1.0916 time to fit residues: 314.1870 Evaluate side-chains 252 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 81 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 131 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 18 HIS B 28 ASN B 105 GLN B 106 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN F 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118003 restraints weight = 21519.796| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.10 r_work: 0.3266 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 18382 Z= 0.254 Angle : 0.684 9.942 25032 Z= 0.338 Chirality : 0.049 0.347 2889 Planarity : 0.004 0.047 3110 Dihedral : 9.328 105.889 3717 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.64 % Allowed : 16.82 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.87 (0.18), residues: 2148 helix: 1.59 (0.26), residues: 363 sheet: -1.15 (0.20), residues: 591 loop : -0.92 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 96 HIS 0.012 0.002 HIS A 18 PHE 0.017 0.002 PHE F 63 TYR 0.021 0.002 TYR L 49 ARG 0.005 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 16) link_NAG-ASN : angle 2.98008 ( 48) link_ALPHA1-6 : bond 0.00976 ( 9) link_ALPHA1-6 : angle 1.67456 ( 27) link_BETA1-4 : bond 0.00520 ( 24) link_BETA1-4 : angle 1.91000 ( 72) link_ALPHA1-3 : bond 0.01207 ( 9) link_ALPHA1-3 : angle 2.18450 ( 27) hydrogen bonds : bond 0.03983 ( 625) hydrogen bonds : angle 5.01667 ( 1761) SS BOND : bond 0.00605 ( 26) SS BOND : angle 2.26298 ( 52) covalent geometry : bond 0.00611 (18298) covalent geometry : angle 0.65210 (24806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 28 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.7996 (p0) REVERT: C 201 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7701 (ttp-110) REVERT: D 37 ASP cc_start: 0.8582 (t70) cc_final: 0.8190 (t70) REVERT: D 54 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7270 (ttp-110) REVERT: G 50 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: G 53 ASP cc_start: 0.8364 (p0) cc_final: 0.8153 (p0) REVERT: G 77 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: G 156 GLN cc_start: 0.8538 (pm20) cc_final: 0.8180 (pp30) REVERT: G 172 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8484 (mm-30) REVERT: G 276 LYS cc_start: 0.8762 (mptp) cc_final: 0.8410 (mppt) REVERT: I 22 TYR cc_start: 0.9376 (m-80) cc_final: 0.8938 (m-80) REVERT: I 54 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7591 (mtt90) REVERT: I 170 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6325 (mmt180) REVERT: L 79 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7400 (mt-10) REVERT: E 13 MET cc_start: 0.7165 (mmt) cc_final: 0.5947 (ptt) REVERT: E 56 TYR cc_start: 0.8947 (t80) cc_final: 0.8683 (t80) REVERT: E 86 ASP cc_start: 0.8484 (m-30) cc_final: 0.8176 (m-30) REVERT: F 13 MET cc_start: 0.7079 (mmt) cc_final: 0.6013 (ptt) REVERT: F 22 CYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8197 (t) REVERT: K 27 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7509 (pm20) outliers start: 50 outliers final: 23 residues processed: 248 average time/residue: 1.0891 time to fit residues: 307.8259 Evaluate side-chains 245 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 72 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 131 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 28 ASN B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 34 ASN F 105 GLN K 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.150924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122501 restraints weight = 21308.184| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.09 r_work: 0.3358 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18382 Z= 0.125 Angle : 0.591 9.747 25032 Z= 0.292 Chirality : 0.045 0.333 2889 Planarity : 0.004 0.045 3110 Dihedral : 8.799 105.705 3717 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.00 % Allowed : 17.88 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.74 (0.18), residues: 2148 helix: 1.76 (0.26), residues: 365 sheet: -1.07 (0.20), residues: 585 loop : -0.87 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 96 HIS 0.010 0.001 HIS A 18 PHE 0.016 0.001 PHE F 63 TYR 0.020 0.001 TYR L 49 ARG 0.009 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 16) link_NAG-ASN : angle 2.68996 ( 48) link_ALPHA1-6 : bond 0.00940 ( 9) link_ALPHA1-6 : angle 1.67683 ( 27) link_BETA1-4 : bond 0.00446 ( 24) link_BETA1-4 : angle 1.77899 ( 72) link_ALPHA1-3 : bond 0.01150 ( 9) link_ALPHA1-3 : angle 2.06766 ( 27) hydrogen bonds : bond 0.03438 ( 625) hydrogen bonds : angle 4.83426 ( 1761) SS BOND : bond 0.00460 ( 26) SS BOND : angle 1.91036 ( 52) covalent geometry : bond 0.00279 (18298) covalent geometry : angle 0.56048 (24806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8465 (tt) REVERT: C 201 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.7656 (ttp-110) REVERT: D 37 ASP cc_start: 0.8549 (t70) cc_final: 0.8117 (t70) REVERT: G 53 ASP cc_start: 0.8160 (p0) cc_final: 0.7920 (p0) REVERT: G 77 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: G 156 GLN cc_start: 0.8505 (pm20) cc_final: 0.8172 (pp30) REVERT: G 172 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8455 (mm-30) REVERT: G 276 LYS cc_start: 0.8674 (mptp) cc_final: 0.8383 (mppt) REVERT: I 22 TYR cc_start: 0.9351 (m-80) cc_final: 0.8921 (m-80) REVERT: E 13 MET cc_start: 0.7185 (mmt) cc_final: 0.6012 (ptt) REVERT: E 56 TYR cc_start: 0.8920 (t80) cc_final: 0.8658 (t80) REVERT: E 86 ASP cc_start: 0.8515 (m-30) cc_final: 0.8211 (m-30) REVERT: F 13 MET cc_start: 0.7099 (mmt) cc_final: 0.6043 (ptt) REVERT: K 27 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7504 (pm20) outliers start: 38 outliers final: 25 residues processed: 255 average time/residue: 1.0648 time to fit residues: 312.2891 Evaluate side-chains 255 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 179 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 28 ASN B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 34 ASN F 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121520 restraints weight = 21273.302| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.08 r_work: 0.3347 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18382 Z= 0.153 Angle : 0.603 9.616 25032 Z= 0.298 Chirality : 0.046 0.334 2889 Planarity : 0.004 0.045 3110 Dihedral : 8.651 105.750 3717 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.90 % Allowed : 17.88 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.71 (0.18), residues: 2148 helix: 1.78 (0.26), residues: 365 sheet: -1.06 (0.20), residues: 585 loop : -0.84 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 96 HIS 0.012 0.001 HIS A 18 PHE 0.016 0.001 PHE F 63 TYR 0.020 0.001 TYR L 49 ARG 0.009 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 16) link_NAG-ASN : angle 2.70084 ( 48) link_ALPHA1-6 : bond 0.00972 ( 9) link_ALPHA1-6 : angle 1.68411 ( 27) link_BETA1-4 : bond 0.00457 ( 24) link_BETA1-4 : angle 1.75916 ( 72) link_ALPHA1-3 : bond 0.01147 ( 9) link_ALPHA1-3 : angle 2.01622 ( 27) hydrogen bonds : bond 0.03528 ( 625) hydrogen bonds : angle 4.82435 ( 1761) SS BOND : bond 0.00467 ( 26) SS BOND : angle 1.95931 ( 52) covalent geometry : bond 0.00358 (18298) covalent geometry : angle 0.57303 (24806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8494 (tt) REVERT: B 61 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8016 (mp0) REVERT: C 201 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7646 (ttp-110) REVERT: D 37 ASP cc_start: 0.8538 (t70) cc_final: 0.8134 (t70) REVERT: G 77 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: G 156 GLN cc_start: 0.8519 (pm20) cc_final: 0.8185 (pp30) REVERT: G 172 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8452 (mm-30) REVERT: G 276 LYS cc_start: 0.8663 (mptp) cc_final: 0.8316 (mppt) REVERT: I 22 TYR cc_start: 0.9360 (m-80) cc_final: 0.8931 (m-80) REVERT: I 170 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6215 (mmt180) REVERT: E 13 MET cc_start: 0.7176 (mmt) cc_final: 0.6048 (ptt) REVERT: E 56 TYR cc_start: 0.8929 (t80) cc_final: 0.8669 (t80) REVERT: E 86 ASP cc_start: 0.8539 (m-30) cc_final: 0.8243 (m-30) REVERT: F 13 MET cc_start: 0.7120 (mmt) cc_final: 0.6084 (ptt) REVERT: K 27 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7527 (pm20) outliers start: 36 outliers final: 24 residues processed: 246 average time/residue: 1.1117 time to fit residues: 312.0527 Evaluate side-chains 252 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 194 optimal weight: 0.0040 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 28 ASN B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN F 105 GLN K 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121485 restraints weight = 21183.171| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.07 r_work: 0.3348 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18382 Z= 0.157 Angle : 0.605 9.523 25032 Z= 0.298 Chirality : 0.046 0.331 2889 Planarity : 0.004 0.044 3110 Dihedral : 8.532 105.932 3717 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.95 % Allowed : 17.72 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.71 (0.18), residues: 2148 helix: 1.78 (0.26), residues: 365 sheet: -1.06 (0.20), residues: 585 loop : -0.84 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 96 HIS 0.012 0.001 HIS A 18 PHE 0.016 0.001 PHE F 63 TYR 0.020 0.001 TYR L 49 ARG 0.009 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 16) link_NAG-ASN : angle 2.66253 ( 48) link_ALPHA1-6 : bond 0.00974 ( 9) link_ALPHA1-6 : angle 1.69046 ( 27) link_BETA1-4 : bond 0.00459 ( 24) link_BETA1-4 : angle 1.75255 ( 72) link_ALPHA1-3 : bond 0.01112 ( 9) link_ALPHA1-3 : angle 1.95811 ( 27) hydrogen bonds : bond 0.03543 ( 625) hydrogen bonds : angle 4.82368 ( 1761) SS BOND : bond 0.00466 ( 26) SS BOND : angle 1.94313 ( 52) covalent geometry : bond 0.00367 (18298) covalent geometry : angle 0.57544 (24806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12051.25 seconds wall clock time: 208 minutes 53.53 seconds (12533.53 seconds total)