Starting phenix.real_space_refine on Mon Nov 18 23:23:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx3_41676/11_2024/8tx3_41676.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx3_41676/11_2024/8tx3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx3_41676/11_2024/8tx3_41676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx3_41676/11_2024/8tx3_41676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx3_41676/11_2024/8tx3_41676.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx3_41676/11_2024/8tx3_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.44, per 1000 atoms: 0.64 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: 5.09 Conformation dependent library (CDL) restraints added in 2.3 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: 2.93 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: 6.38 Time building geometry restraints manager: 5.62 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: 2.820 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 42.460 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.950 ------------------------------------------------------------------------------- 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 : 0.005 0.087 18298 Z= 0.350 Angle : 0.869 10.752 24806 Z= 0.472 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 *********************** 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 : 1.922 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: 1.0673 time to fit residues: 358.4009 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 : 1.936 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 18298 Z= 0.391 Angle : 0.725 14.633 24806 Z= 0.359 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 *********************** 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 : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.6933 (m-40) cc_final: 0.6699 (OUTLIER) REVERT: A 75 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7815 (pp30) REVERT: C 144 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.6957 (m110) REVERT: D 27 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: G 144 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7132 (m110) REVERT: G 156 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: G 321 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7436 (ttt180) REVERT: I 79 ASP cc_start: 0.8112 (m-30) cc_final: 0.7852 (m-30) REVERT: I 170 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.5730 (mmt180) REVERT: E 56 TYR cc_start: 0.8876 (t80) cc_final: 0.8661 (t80) REVERT: F 17 SER cc_start: 0.7892 (p) cc_final: 0.7634 (m) outliers start: 38 outliers final: 14 residues processed: 249 average time/residue: 1.1924 time to fit residues: 337.3435 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 : 1.932 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 153 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 105 GLN C 17 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18298 Z= 0.177 Angle : 0.569 8.862 24806 Z= 0.283 Chirality : 0.045 0.481 2889 Planarity : 0.004 0.051 3110 Dihedral : 13.243 106.702 3717 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.69 % Allowed : 12.03 % Favored : 86.29 % 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: 1.84 (0.27), residues: 355 sheet: -1.02 (0.21), residues: 609 loop : -0.84 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.008 0.001 HIS B 159 PHE 0.016 0.001 PHE D 9 TYR 0.021 0.001 TYR L 49 ARG 0.010 0.000 ARG C 201 *********************** 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 276 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.6876 (m-40) cc_final: 0.6650 (OUTLIER) REVERT: B 61 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7500 (mp0) REVERT: C 77 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: D 37 ASP cc_start: 0.8307 (t70) cc_final: 0.7902 (t70) REVERT: D 115 MET cc_start: 0.8765 (tpt) cc_final: 0.8065 (tpt) REVERT: G 53 ASP cc_start: 0.7713 (p0) cc_final: 0.7402 (p0) REVERT: G 144 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7064 (m110) REVERT: G 156 GLN cc_start: 0.8115 (pm20) cc_final: 0.7891 (pp30) REVERT: I 79 ASP cc_start: 0.8055 (m-30) cc_final: 0.7823 (m-30) REVERT: E 13 MET cc_start: 0.7018 (mmt) cc_final: 0.6087 (ptt) REVERT: F 17 SER cc_start: 0.7852 (p) cc_final: 0.7594 (m) outliers start: 32 outliers final: 10 residues processed: 261 average time/residue: 1.1059 time to fit residues: 329.8486 Evaluate side-chains 226 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 105 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 26 HIS ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN I 78 GLN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 34 ASN L 90 GLN K 34 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 18298 Z= 0.265 Angle : 0.601 9.736 24806 Z= 0.301 Chirality : 0.047 0.412 2889 Planarity : 0.004 0.047 3110 Dihedral : 11.810 106.764 3717 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.16 % Allowed : 13.66 % Favored : 84.18 % 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: -0.68 (0.18), residues: 2148 helix: 1.87 (0.27), residues: 355 sheet: -1.03 (0.20), residues: 609 loop : -0.82 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.010 0.002 HIS I 159 PHE 0.013 0.001 PHE D 9 TYR 0.021 0.001 TYR L 49 ARG 0.005 0.000 ARG B 54 *********************** 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 258 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.6867 (m-40) cc_final: 0.6565 (OUTLIER) REVERT: A 244 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8419 (tt) REVERT: D 37 ASP cc_start: 0.8316 (t70) cc_final: 0.7941 (t70) REVERT: G 144 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7055 (m110) REVERT: G 156 GLN cc_start: 0.8158 (pm20) cc_final: 0.7916 (pp30) REVERT: I 79 ASP cc_start: 0.8065 (m-30) cc_final: 0.7824 (m-30) REVERT: I 170 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.5717 (mmt180) REVERT: E 13 MET cc_start: 0.7089 (mmt) cc_final: 0.6107 (ptt) outliers start: 41 outliers final: 19 residues processed: 242 average time/residue: 1.1499 time to fit residues: 316.9503 Evaluate side-chains 228 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain G residue 77 ASP 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 I residue 73 VAL 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 33 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN I 78 GLN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 18298 Z= 0.398 Angle : 0.667 8.279 24806 Z= 0.335 Chirality : 0.049 0.383 2889 Planarity : 0.004 0.047 3110 Dihedral : 11.021 106.230 3717 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.90 % Allowed : 13.98 % Favored : 83.12 % 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: -0.88 (0.18), residues: 2148 helix: 1.56 (0.27), residues: 360 sheet: -1.18 (0.20), residues: 612 loop : -0.88 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 96 HIS 0.010 0.002 HIS I 159 PHE 0.014 0.002 PHE D 9 TYR 0.022 0.002 TYR L 49 ARG 0.005 0.000 ARG B 54 *********************** 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 268 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8430 (tt) REVERT: B 61 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: G 144 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7049 (m110) REVERT: G 156 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: I 79 ASP cc_start: 0.8082 (m-30) cc_final: 0.7834 (m-30) REVERT: I 153 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.5678 (mpp80) REVERT: I 170 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.5942 (mmt180) REVERT: F 99 ASN cc_start: 0.9042 (p0) cc_final: 0.8788 (p0) REVERT: K 27 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.7500 (pm20) outliers start: 55 outliers final: 25 residues processed: 242 average time/residue: 1.1439 time to fit residues: 315.7711 Evaluate side-chains 231 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL 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 144 ASN Chi-restraints excluded: chain G residue 156 GLN 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 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 25 SER 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 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 68 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18298 Z= 0.194 Angle : 0.560 8.317 24806 Z= 0.282 Chirality : 0.045 0.348 2889 Planarity : 0.004 0.044 3110 Dihedral : 9.839 105.185 3717 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.16 % Allowed : 15.40 % Favored : 82.44 % 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: -0.70 (0.18), residues: 2148 helix: 1.81 (0.27), residues: 360 sheet: -1.09 (0.20), residues: 609 loop : -0.78 (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 B 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 *********************** 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: 41 poor density : 227 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: B 128 GLU cc_start: 0.7818 (mp0) cc_final: 0.7413 (mp0) REVERT: C 77 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: G 156 GLN cc_start: 0.8284 (pm20) cc_final: 0.7991 (pp30) REVERT: I 22 TYR cc_start: 0.9283 (m-80) cc_final: 0.9025 (m-80) REVERT: I 79 ASP cc_start: 0.8062 (m-30) cc_final: 0.7813 (m-30) REVERT: E 13 MET cc_start: 0.7041 (mmt) cc_final: 0.6124 (ptt) outliers start: 41 outliers final: 18 residues processed: 249 average time/residue: 1.1418 time to fit residues: 323.8110 Evaluate side-chains 230 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 313 THR Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C 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 159 HIS 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 15 LEU 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 K residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 202 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 18298 Z= 0.326 Angle : 0.621 8.800 24806 Z= 0.313 Chirality : 0.047 0.355 2889 Planarity : 0.004 0.045 3110 Dihedral : 9.481 104.997 3717 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.22 % Allowed : 16.09 % Favored : 81.70 % 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: -0.81 (0.18), residues: 2148 helix: 1.68 (0.26), residues: 363 sheet: -1.12 (0.20), residues: 585 loop : -0.90 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 96 HIS 0.010 0.002 HIS B 159 PHE 0.012 0.001 PHE D 9 TYR 0.021 0.001 TYR L 49 ARG 0.007 0.000 ARG B 54 *********************** 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 258 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: G 156 GLN cc_start: 0.8309 (pm20) cc_final: 0.7950 (pp30) REVERT: I 22 TYR cc_start: 0.9314 (m-80) cc_final: 0.8907 (m-80) REVERT: I 79 ASP cc_start: 0.8034 (m-30) cc_final: 0.7796 (m-30) REVERT: I 170 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6022 (mmt180) REVERT: E 13 MET cc_start: 0.7053 (mmt) cc_final: 0.6138 (ptt) REVERT: F 22 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7504 (t) REVERT: F 99 ASN cc_start: 0.9049 (p0) cc_final: 0.8842 (p0) REVERT: K 27 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7541 (pm20) outliers start: 42 outliers final: 21 residues processed: 239 average time/residue: 1.1850 time to fit residues: 326.2174 Evaluate side-chains 232 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 313 THR 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 77 ASP Chi-restraints excluded: chain C residue 203 THR 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 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 22 CYS Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN K 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18298 Z= 0.216 Angle : 0.569 8.136 24806 Z= 0.288 Chirality : 0.045 0.336 2889 Planarity : 0.004 0.044 3110 Dihedral : 8.970 104.716 3717 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.11 % Allowed : 16.61 % Favored : 81.28 % 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: -0.75 (0.18), residues: 2148 helix: 1.78 (0.27), residues: 363 sheet: -1.08 (0.21), residues: 555 loop : -0.90 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 96 HIS 0.011 0.001 HIS A 18 PHE 0.020 0.001 PHE F 63 TYR 0.020 0.001 TYR L 49 ARG 0.012 0.000 ARG C 201 *********************** 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 265 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8387 (tt) REVERT: C 77 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: D 37 ASP cc_start: 0.8285 (t70) cc_final: 0.7871 (t70) REVERT: G 156 GLN cc_start: 0.8310 (pm20) cc_final: 0.7958 (pp30) REVERT: I 22 TYR cc_start: 0.9290 (m-80) cc_final: 0.8887 (m-80) REVERT: I 79 ASP cc_start: 0.7994 (m-30) cc_final: 0.7749 (m-30) REVERT: E 13 MET cc_start: 0.7062 (mmt) cc_final: 0.6169 (ptt) REVERT: K 27 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7512 (pm20) outliers start: 40 outliers final: 24 residues processed: 248 average time/residue: 1.1371 time to fit residues: 321.9546 Evaluate side-chains 246 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR 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 77 ASP Chi-restraints excluded: chain C residue 111 LEU 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 G residue 260 ILE Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 159 HIS 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 25 SER 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 22 CYS Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.1980 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 B 106 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** 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 L 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 18298 Z= 0.283 Angle : 0.598 8.541 24806 Z= 0.303 Chirality : 0.046 0.340 2889 Planarity : 0.004 0.045 3110 Dihedral : 8.828 105.053 3717 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.37 % Allowed : 16.51 % Favored : 81.12 % 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: -0.78 (0.18), residues: 2148 helix: 1.71 (0.26), residues: 365 sheet: -1.10 (0.21), residues: 555 loop : -0.90 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.011 0.002 HIS A 18 PHE 0.019 0.001 PHE F 63 TYR 0.020 0.001 TYR L 49 ARG 0.010 0.000 ARG C 201 *********************** 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 266 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 2.105 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: 0.8787 (OUTLIER) cc_final: 0.8440 (tt) REVERT: C 77 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: G 50 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: G 156 GLN cc_start: 0.8336 (pm20) cc_final: 0.7993 (pp30) REVERT: I 22 TYR cc_start: 0.9310 (m-80) cc_final: 0.8904 (m-80) REVERT: I 79 ASP cc_start: 0.7987 (m-30) cc_final: 0.7742 (m-30) REVERT: I 170 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6086 (mmt180) REVERT: E 13 MET cc_start: 0.7069 (mmt) cc_final: 0.6167 (ptt) REVERT: J 4 MET cc_start: 0.8644 (tpt) cc_final: 0.8403 (tpt) REVERT: K 27 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7530 (pm20) outliers start: 45 outliers final: 29 residues processed: 248 average time/residue: 1.1469 time to fit residues: 323.7333 Evaluate side-chains 250 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain G residue 50 GLU 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 G residue 260 ILE 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 70 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 SER 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 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 F residue 25 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 209 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN K 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18298 Z= 0.183 Angle : 0.557 8.528 24806 Z= 0.282 Chirality : 0.045 0.324 2889 Planarity : 0.004 0.050 3110 Dihedral : 8.368 104.602 3717 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.90 % Allowed : 17.25 % Favored : 80.85 % 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: -0.65 (0.18), residues: 2148 helix: 1.95 (0.27), residues: 359 sheet: -1.01 (0.21), residues: 555 loop : -0.86 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 96 HIS 0.011 0.001 HIS A 18 PHE 0.019 0.001 PHE F 63 TYR 0.019 0.001 TYR L 49 ARG 0.015 0.000 ARG C 201 ********************** 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 254 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 2.090 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: 0.8750 (OUTLIER) cc_final: 0.8429 (tt) REVERT: C 77 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: D 54 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7320 (ttp-110) REVERT: G 156 GLN cc_start: 0.8357 (pm20) cc_final: 0.8019 (pp30) REVERT: I 22 TYR cc_start: 0.9287 (m-80) cc_final: 0.8867 (m-80) REVERT: I 79 ASP cc_start: 0.7991 (m-30) cc_final: 0.7752 (m-30) REVERT: E 13 MET cc_start: 0.7053 (mmt) cc_final: 0.6176 (ptt) REVERT: F 13 MET cc_start: 0.6989 (mmt) cc_final: 0.6177 (ptt) REVERT: K 27 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7543 (pm20) outliers start: 36 outliers final: 26 residues processed: 240 average time/residue: 1.1328 time to fit residues: 312.1279 Evaluate side-chains 239 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 260 ILE 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 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 25 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 197 GLN B 105 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** C 290 ASN ** 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 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 = 0.3798 r_free = 0.3798 target = 0.149314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120677 restraints weight = 21269.485| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.08 r_work: 0.3302 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 18298 Z= 0.278 Angle : 0.598 8.691 24806 Z= 0.302 Chirality : 0.046 0.334 2889 Planarity : 0.004 0.049 3110 Dihedral : 8.395 104.972 3717 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.11 % Allowed : 17.09 % Favored : 80.80 % 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: -0.72 (0.18), residues: 2148 helix: 1.77 (0.26), residues: 365 sheet: -1.05 (0.21), residues: 555 loop : -0.87 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 96 HIS 0.012 0.002 HIS A 18 PHE 0.019 0.001 PHE F 63 TYR 0.020 0.001 TYR L 49 ARG 0.014 0.000 ARG C 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6301.59 seconds wall clock time: 114 minutes 22.33 seconds (6862.33 seconds total)