Starting phenix.real_space_refine on Sat Jul 4 07:05:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.map" model { file = "/net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3b_22655/07_2026/7k3b_22655.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 11901 2.51 5 N 3192 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19038 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "D" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "E" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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 chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.28, per 1000 atoms: 0.28 Number of scatterers: 19038 At special positions: 0 Unit cell: (184.87, 186.2, 127.68, 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 3864 8.00 N 3192 7.00 C 11901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.02 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " 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 ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " 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 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 T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 834.9 milliseconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4404 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 63 sheets defined 16.8% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.550A 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 195 Processing helix chain 'B' and resid 75 through 125 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.244A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 75 through 125 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 75 through 125 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.669A pdb=" N GLU G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.557A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.689A pdb=" N GLU I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY J 200 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR J 201 " --> pdb=" O SER J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.763A pdb=" N LEU K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.514A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.697A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.710A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.668A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.578A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (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 39 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 54 removed outlier: 5.698A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (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 61 Processing sheet with id=AB9, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.044A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (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: 7.669A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.517A pdb=" N LYS D 62 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.698A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.670A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD8, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 303 through 304 removed outlier: 3.646A pdb=" N LYS F 62 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.294A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.601A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL G 138 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU G 184 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU G 140 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER G 182 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN G 142 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU G 180 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.291A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 197 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.454A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.703A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 150 through 155 Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL J 191 " --> pdb=" O HIS J 174 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 161 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.562A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 17 through 22 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.531A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR K 178 " --> pdb=" O ASN K 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 158 through 160 removed outlier: 4.438A pdb=" N TRP K 153 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS K 199 " --> pdb=" O LYS K 212 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS K 212 " --> pdb=" O CYS K 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 201 " --> pdb=" O VAL K 210 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL K 210 " --> pdb=" O VAL K 201 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL L 191 " --> pdb=" O HIS L 174 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 161 through 164 779 hydrogen bonds defined for protein. 1944 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: 3.57 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6038 1.34 - 1.46: 4512 1.46 - 1.58: 8770 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 19434 Sorted by residual: bond pdb=" C3 BMA R 3 " pdb=" C4 BMA R 3 " ideal model delta sigma weight residual 1.541 1.503 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C3 BMA O 3 " pdb=" C4 BMA O 3 " ideal model delta sigma weight residual 1.541 1.503 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C3 BMA U 3 " pdb=" C4 BMA U 3 " ideal model delta sigma weight residual 1.541 1.504 0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C3 MAN R 4 " pdb=" O3 MAN R 4 " ideal model delta sigma weight residual 1.408 1.442 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C3 MAN O 4 " pdb=" O3 MAN O 4 " ideal model delta sigma weight residual 1.408 1.441 -0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 19429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 24943 1.46 - 2.92: 1152 2.92 - 4.37: 228 4.37 - 5.83: 55 5.83 - 7.29: 40 Bond angle restraints: 26418 Sorted by residual: angle pdb=" C HIS G 194 " pdb=" N LYS G 195 " pdb=" CA LYS G 195 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLY B 50 " pdb=" N LYS B 51 " pdb=" CA LYS B 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.82e+00 angle pdb=" C GLY F 50 " pdb=" N LYS F 51 " pdb=" CA LYS F 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.81e+00 angle pdb=" C GLY D 50 " pdb=" N LYS D 51 " pdb=" CA LYS D 51 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.79e+00 angle pdb=" C GLY K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.54 126.47 -4.93 1.91e+00 2.74e-01 6.65e+00 ... (remaining 26413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10281 17.31 - 34.62: 842 34.62 - 51.93: 120 51.93 - 69.23: 30 69.23 - 86.54: 16 Dihedral angle restraints: 11289 sinusoidal: 4419 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 37.38 55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 40.51 52.49 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA GLN I 81 " pdb=" C GLN I 81 " pdb=" N ALA I 82 " pdb=" CA ALA I 82 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 11286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2631 0.069 - 0.137: 489 0.137 - 0.206: 15 0.206 - 0.274: 15 0.274 - 0.343: 3 Chirality restraints: 3153 Sorted by residual: chirality pdb=" C1 NAG E 401 " pdb=" ND2 ASN E 22 " pdb=" C2 NAG E 401 " pdb=" O5 NAG E 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 22 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 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 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3150 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 194 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO J 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 195 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 194 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO H 195 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 195 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 195 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 194 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO L 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 195 " 0.021 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 867 2.70 - 3.25: 18430 3.25 - 3.80: 31238 3.80 - 4.35: 38786 4.35 - 4.90: 67752 Nonbonded interactions: 157073 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.155 3.040 nonbonded pdb=" ND2 ASN K 163 " pdb=" O THR K 185 " model vdw 2.183 3.120 nonbonded pdb=" O SER K 92 " pdb=" OG SER K 100 " model vdw 2.184 3.040 nonbonded pdb=" O SER I 92 " pdb=" OG SER I 100 " model vdw 2.200 3.040 nonbonded pdb=" O SER G 92 " pdb=" OG SER G 100 " model vdw 2.202 3.040 ... (remaining 157068 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.390 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.730 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.008 0.047 19509 Z= 0.349 Angle : 0.804 9.482 26619 Z= 0.399 Chirality : 0.052 0.343 3153 Planarity : 0.004 0.038 3309 Dihedral : 12.854 86.542 6813 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2352 helix: 2.41 (0.30), residues: 282 sheet: -0.34 (0.18), residues: 771 loop : -0.51 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 103 TYR 0.014 0.001 TYR I 178 PHE 0.019 0.002 PHE I 121 TRP 0.013 0.001 TRP I 153 HIS 0.004 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.35 (19434) covalent geometry : angle 0.78022 / 0.39 (26418) SS BOND : bond 0.00651 / 0.50 ( 24) SS BOND : angle 0.95608 / 0.74 ( 48) hydrogen bonds : bond 0.12277 / 7.67 ( 731) hydrogen bonds : angle 6.65227 / 4.76 ( 1944) link_ALPHA1-2 : bond 0.00095 / 0.05 ( 3) link_ALPHA1-2 : angle 1.83065 / 1.63 ( 9) link_ALPHA1-3 : bond 0.00230 / 0.16 ( 9) link_ALPHA1-3 : angle 3.06202 / 2.17 ( 27) link_ALPHA1-6 : bond 0.00523 / 0.38 ( 9) link_ALPHA1-6 : angle 2.62627 / 2.07 ( 27) link_BETA1-4 : bond 0.00361 / 0.27 ( 15) link_BETA1-4 : angle 1.88550 / 1.37 ( 45) link_NAG-ASN : bond 0.00660 / 0.51 ( 15) link_NAG-ASN : angle 3.10056 / 1.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.8421 (mmm) cc_final: 0.8187 (mtp) REVERT: A 320 MET cc_start: 0.7235 (ptp) cc_final: 0.7031 (ptp) REVERT: B 67 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7823 (tp30) REVERT: B 77 ILE cc_start: 0.9202 (mm) cc_final: 0.8972 (mp) REVERT: B 86 ASP cc_start: 0.8217 (t0) cc_final: 0.7846 (t0) REVERT: D 67 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7870 (tp30) REVERT: D 74 GLU cc_start: 0.7380 (mp0) cc_final: 0.7037 (mp0) REVERT: F 67 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7596 (tp30) REVERT: F 86 ASP cc_start: 0.8064 (t0) cc_final: 0.7814 (t0) REVERT: F 105 GLN cc_start: 0.8478 (tp40) cc_final: 0.8172 (tp40) REVERT: G 107 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8415 (mtpp) REVERT: G 141 LEU cc_start: 0.8417 (mp) cc_final: 0.8106 (mp) REVERT: G 144 PHE cc_start: 0.8354 (p90) cc_final: 0.7903 (p90) REVERT: G 145 TYR cc_start: 0.6973 (t80) cc_final: 0.6651 (t80) REVERT: G 178 TYR cc_start: 0.6600 (m-10) cc_final: 0.6364 (m-10) REVERT: H 89 ASP cc_start: 0.8477 (p0) cc_final: 0.8143 (p0) REVERT: H 164 TRP cc_start: 0.7486 (m100) cc_final: 0.7098 (m100) REVERT: H 205 ILE cc_start: 0.7319 (mp) cc_final: 0.7069 (mp) REVERT: H 210 HIS cc_start: 0.7860 (t-170) cc_final: 0.7340 (t-170) REVERT: H 214 ASN cc_start: 0.7863 (t0) cc_final: 0.7497 (t0) REVERT: H 219 LYS cc_start: 0.7992 (tttm) cc_final: 0.7503 (ttpp) REVERT: I 141 LEU cc_start: 0.8228 (mp) cc_final: 0.7892 (tp) REVERT: I 180 LEU cc_start: 0.8816 (tt) cc_final: 0.8604 (tp) REVERT: J 164 TRP cc_start: 0.7638 (m100) cc_final: 0.6901 (m100) REVERT: J 205 ILE cc_start: 0.7366 (mp) cc_final: 0.6962 (mp) REVERT: J 219 LYS cc_start: 0.7902 (tttm) cc_final: 0.7464 (ttpp) REVERT: K 50 ILE cc_start: 0.9024 (pt) cc_final: 0.8808 (mt) REVERT: K 68 LYS cc_start: 0.8779 (tttt) cc_final: 0.7713 (tptt) REVERT: K 108 LEU cc_start: 0.8969 (mp) cc_final: 0.8556 (tt) REVERT: K 128 GLU cc_start: 0.6997 (mp0) cc_final: 0.6670 (mp0) REVERT: K 150 LYS cc_start: 0.6842 (tppt) cc_final: 0.6423 (tmtt) REVERT: L 132 PHE cc_start: 0.7825 (m-80) cc_final: 0.7436 (m-10) REVERT: L 153 LYS cc_start: 0.7750 (tptm) cc_final: 0.7135 (tptt) REVERT: L 164 TRP cc_start: 0.7412 (m100) cc_final: 0.6515 (m100) REVERT: L 179 VAL cc_start: 0.8917 (t) cc_final: 0.8620 (p) REVERT: L 205 ILE cc_start: 0.7300 (mp) cc_final: 0.6666 (mp) REVERT: L 210 HIS cc_start: 0.7432 (t-170) cc_final: 0.7212 (t-170) REVERT: L 219 LYS cc_start: 0.7904 (tttm) cc_final: 0.7588 (ttpp) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.1520 time to fit residues: 94.1411 Evaluate side-chains 275 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN A 322 ASN C 197 GLN E 197 GLN E 322 ASN G 53 ASN ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.087702 restraints weight = 33876.976| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.18 r_work: 0.2738 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19509 Z= 0.174 Angle : 0.660 9.529 26619 Z= 0.324 Chirality : 0.048 0.365 3153 Planarity : 0.004 0.044 3309 Dihedral : 4.735 22.044 2556 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.25 % Allowed : 8.14 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2352 helix: 2.60 (0.30), residues: 282 sheet: -0.32 (0.18), residues: 780 loop : -0.57 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.024 0.002 TYR K 178 PHE 0.017 0.002 PHE I 123 TRP 0.028 0.001 TRP K 153 HIS 0.005 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (19434) covalent geometry : angle 0.63693 / 0.32 (26418) SS BOND : bond 0.00646 / 0.48 ( 24) SS BOND : angle 1.30390 / 0.99 ( 48) hydrogen bonds : bond 0.03272 / 2.18 ( 731) hydrogen bonds : angle 5.68474 / 4.06 ( 1944) link_ALPHA1-2 : bond 0.00282 / 0.14 ( 3) link_ALPHA1-2 : angle 1.51232 / 1.35 ( 9) link_ALPHA1-3 : bond 0.00103 / 0.07 ( 9) link_ALPHA1-3 : angle 2.44979 / 1.69 ( 27) link_ALPHA1-6 : bond 0.00464 / 0.34 ( 9) link_ALPHA1-6 : angle 1.81211 / 1.37 ( 27) link_BETA1-4 : bond 0.00348 / 0.27 ( 15) link_BETA1-4 : angle 1.76912 / 1.28 ( 45) link_NAG-ASN : bond 0.00711 / 0.55 ( 15) link_NAG-ASN : angle 2.86233 / 1.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 319 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8129 (tt0) cc_final: 0.7266 (tt0) REVERT: A 208 ARG cc_start: 0.7906 (ptp-170) cc_final: 0.7593 (ptp-170) REVERT: A 320 MET cc_start: 0.7473 (ptp) cc_final: 0.6981 (ptp) REVERT: A 322 ASN cc_start: 0.6632 (t0) cc_final: 0.6086 (t0) REVERT: B 67 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8287 (tp30) REVERT: B 74 GLU cc_start: 0.7891 (mp0) cc_final: 0.7276 (mp0) REVERT: B 77 ILE cc_start: 0.9166 (mm) cc_final: 0.8965 (mp) REVERT: B 86 ASP cc_start: 0.8882 (t0) cc_final: 0.8449 (t0) REVERT: C 123 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8166 (mt-10) REVERT: C 260 MET cc_start: 0.8926 (mtp) cc_final: 0.8515 (mtp) REVERT: D 67 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8255 (tp30) REVERT: D 74 GLU cc_start: 0.8058 (mp0) cc_final: 0.7487 (mp0) REVERT: F 67 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8055 (tp30) REVERT: F 74 GLU cc_start: 0.7977 (mp0) cc_final: 0.7573 (mp0) REVERT: F 86 ASP cc_start: 0.8910 (t0) cc_final: 0.8519 (t0) REVERT: F 105 GLN cc_start: 0.8687 (tp40) cc_final: 0.8333 (tp40) REVERT: G 145 TYR cc_start: 0.7045 (t80) cc_final: 0.6671 (t80) REVERT: H 87 ARG cc_start: 0.8317 (mtm180) cc_final: 0.7914 (mtm180) REVERT: H 89 ASP cc_start: 0.8818 (p0) cc_final: 0.8308 (p0) REVERT: H 164 TRP cc_start: 0.7564 (m100) cc_final: 0.7323 (m100) REVERT: H 205 ILE cc_start: 0.7486 (mp) cc_final: 0.7102 (mp) REVERT: H 210 HIS cc_start: 0.7270 (t-170) cc_final: 0.6888 (t-170) REVERT: H 214 ASN cc_start: 0.8145 (t0) cc_final: 0.7891 (t0) REVERT: I 87 ASP cc_start: 0.8488 (t0) cc_final: 0.8163 (t0) REVERT: I 141 LEU cc_start: 0.7967 (mp) cc_final: 0.7723 (tp) REVERT: I 204 GLN cc_start: 0.8143 (mt0) cc_final: 0.7836 (mp10) REVERT: J 83 MET cc_start: 0.8262 (mtp) cc_final: 0.8006 (mtp) REVERT: J 90 ASP cc_start: 0.8995 (m-30) cc_final: 0.8781 (m-30) REVERT: J 164 TRP cc_start: 0.7664 (m100) cc_final: 0.6954 (m100) REVERT: J 205 ILE cc_start: 0.7211 (mp) cc_final: 0.6633 (mm) REVERT: J 210 HIS cc_start: 0.6920 (t-170) cc_final: 0.6690 (t-170) REVERT: K 107 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8515 (mtmm) REVERT: K 108 LEU cc_start: 0.9017 (mp) cc_final: 0.8650 (tt) REVERT: K 128 GLU cc_start: 0.7141 (mp0) cc_final: 0.6804 (mp0) REVERT: K 141 LEU cc_start: 0.8176 (mp) cc_final: 0.7710 (tp) REVERT: K 153 TRP cc_start: 0.4253 (t-100) cc_final: 0.4009 (t-100) REVERT: L 46 GLU cc_start: 0.8292 (tt0) cc_final: 0.8048 (pt0) REVERT: L 132 PHE cc_start: 0.7935 (m-80) cc_final: 0.7691 (m-10) REVERT: L 164 TRP cc_start: 0.7507 (m100) cc_final: 0.6106 (m100) REVERT: L 179 VAL cc_start: 0.8730 (t) cc_final: 0.8384 (p) REVERT: L 205 ILE cc_start: 0.7508 (mp) cc_final: 0.6972 (mm) outliers start: 26 outliers final: 21 residues processed: 328 average time/residue: 0.1392 time to fit residues: 70.6150 Evaluate side-chains 296 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 275 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 39 GLN Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 13 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 218 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN J 165 ASN K 39 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089142 restraints weight = 33976.452| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.20 r_work: 0.2728 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19509 Z= 0.205 Angle : 0.660 10.122 26619 Z= 0.322 Chirality : 0.047 0.358 3153 Planarity : 0.004 0.040 3309 Dihedral : 4.787 23.663 2556 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.58 % Allowed : 11.35 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2352 helix: 2.70 (0.31), residues: 282 sheet: -0.36 (0.18), residues: 792 loop : -0.58 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.031 0.002 TYR K 178 PHE 0.016 0.002 PHE J 132 TRP 0.015 0.001 TRP K 153 HIS 0.006 0.001 HIS L 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (19434) covalent geometry : angle 0.63443 / 0.32 (26418) SS BOND : bond 0.00467 / 0.37 ( 24) SS BOND : angle 2.10627 / 1.61 ( 48) hydrogen bonds : bond 0.03117 / 2.10 ( 731) hydrogen bonds : angle 5.46928 / 3.88 ( 1944) link_ALPHA1-2 : bond 0.00224 / 0.11 ( 3) link_ALPHA1-2 : angle 1.48746 / 1.33 ( 9) link_ALPHA1-3 : bond 0.00167 / 0.12 ( 9) link_ALPHA1-3 : angle 2.36304 / 1.63 ( 27) link_ALPHA1-6 : bond 0.00498 / 0.37 ( 9) link_ALPHA1-6 : angle 1.88928 / 1.44 ( 27) link_BETA1-4 : bond 0.00335 / 0.26 ( 15) link_BETA1-4 : angle 1.70462 / 1.22 ( 45) link_NAG-ASN : bond 0.00699 / 0.54 ( 15) link_NAG-ASN : angle 2.81789 / 1.54 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 296 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 320 MET cc_start: 0.7377 (ptp) cc_final: 0.7024 (ptp) REVERT: A 322 ASN cc_start: 0.6643 (t0) cc_final: 0.6363 (t0) REVERT: B 67 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8280 (tp30) REVERT: B 77 ILE cc_start: 0.9175 (mm) cc_final: 0.8969 (mp) REVERT: B 85 GLU cc_start: 0.8888 (tp30) cc_final: 0.8669 (tp30) REVERT: B 86 ASP cc_start: 0.8887 (t0) cc_final: 0.8411 (t0) REVERT: B 114 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7084 (tm-30) REVERT: C 35 GLU cc_start: 0.8134 (tt0) cc_final: 0.7605 (tt0) REVERT: C 123 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8244 (mt-10) REVERT: C 246 ASN cc_start: 0.9115 (t0) cc_final: 0.8833 (t0) REVERT: C 260 MET cc_start: 0.9021 (mtp) cc_final: 0.8620 (mtp) REVERT: D 67 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8229 (tp30) REVERT: E 31 ASP cc_start: 0.8016 (m-30) cc_final: 0.7582 (m-30) REVERT: F 67 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8120 (tp30) REVERT: F 76 ARG cc_start: 0.9090 (mtp180) cc_final: 0.8858 (mtp180) REVERT: F 86 ASP cc_start: 0.8904 (t0) cc_final: 0.8438 (t0) REVERT: F 105 GLN cc_start: 0.8793 (tp40) cc_final: 0.8438 (tp40) REVERT: G 128 GLU cc_start: 0.7574 (pm20) cc_final: 0.7297 (pm20) REVERT: G 145 TYR cc_start: 0.7073 (t80) cc_final: 0.6652 (t80) REVERT: G 153 TRP cc_start: 0.5461 (m100) cc_final: 0.5110 (m100) REVERT: H 87 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7917 (mtm180) REVERT: H 89 ASP cc_start: 0.8872 (p0) cc_final: 0.8314 (p0) REVERT: H 164 TRP cc_start: 0.7564 (m100) cc_final: 0.7243 (m100) REVERT: H 205 ILE cc_start: 0.7541 (mp) cc_final: 0.7135 (mp) REVERT: H 210 HIS cc_start: 0.7515 (t-170) cc_final: 0.7067 (t-170) REVERT: I 87 ASP cc_start: 0.8423 (t0) cc_final: 0.8078 (t0) REVERT: I 141 LEU cc_start: 0.7965 (mp) cc_final: 0.7736 (tp) REVERT: I 204 GLN cc_start: 0.8231 (mt0) cc_final: 0.7847 (mp10) REVERT: J 83 MET cc_start: 0.8377 (mtp) cc_final: 0.7892 (mtp) REVERT: J 148 LEU cc_start: 0.8395 (mt) cc_final: 0.7890 (tp) REVERT: J 164 TRP cc_start: 0.7723 (m100) cc_final: 0.6903 (m100) REVERT: J 205 ILE cc_start: 0.7176 (mp) cc_final: 0.6611 (mm) REVERT: K 107 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8435 (mtmm) REVERT: K 108 LEU cc_start: 0.9066 (mp) cc_final: 0.8645 (tt) REVERT: K 128 GLU cc_start: 0.7012 (mp0) cc_final: 0.6606 (mp0) REVERT: K 141 LEU cc_start: 0.8159 (mp) cc_final: 0.7685 (tp) REVERT: K 153 TRP cc_start: 0.5167 (t-100) cc_final: 0.4763 (t-100) REVERT: L 132 PHE cc_start: 0.7770 (m-80) cc_final: 0.7445 (m-10) REVERT: L 179 VAL cc_start: 0.8763 (t) cc_final: 0.8420 (p) outliers start: 33 outliers final: 24 residues processed: 309 average time/residue: 0.1349 time to fit residues: 64.7576 Evaluate side-chains 295 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 107 optimal weight: 0.6980 chunk 138 optimal weight: 0.0470 chunk 189 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 322 ASN G 36 HIS G 53 ASN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS I 81 GLN J 209 ASN K 39 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.085915 restraints weight = 33886.803| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.91 r_work: 0.2758 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19509 Z= 0.165 Angle : 0.627 9.319 26619 Z= 0.306 Chirality : 0.047 0.354 3153 Planarity : 0.004 0.038 3309 Dihedral : 4.676 24.134 2556 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.16 % Allowed : 12.74 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2352 helix: 2.80 (0.31), residues: 282 sheet: -0.25 (0.18), residues: 783 loop : -0.61 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 147 TYR 0.024 0.001 TYR K 178 PHE 0.013 0.001 PHE J 132 TRP 0.012 0.001 TRP H 47 HIS 0.012 0.001 HIS I 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (19434) covalent geometry : angle 0.60234 / 0.30 (26418) SS BOND : bond 0.00416 / 0.33 ( 24) SS BOND : angle 1.88902 / 1.44 ( 48) hydrogen bonds : bond 0.02862 / 1.94 ( 731) hydrogen bonds : angle 5.27834 / 3.74 ( 1944) link_ALPHA1-2 : bond 0.00293 / 0.15 ( 3) link_ALPHA1-2 : angle 1.40516 / 1.25 ( 9) link_ALPHA1-3 : bond 0.00162 / 0.12 ( 9) link_ALPHA1-3 : angle 2.33248 / 1.61 ( 27) link_ALPHA1-6 : bond 0.00445 / 0.33 ( 9) link_ALPHA1-6 : angle 1.83599 / 1.39 ( 27) link_BETA1-4 : bond 0.00334 / 0.27 ( 15) link_BETA1-4 : angle 1.59700 / 1.15 ( 45) link_NAG-ASN : bond 0.00688 / 0.53 ( 15) link_NAG-ASN : angle 2.74630 / 1.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8248 (tt0) cc_final: 0.7565 (tt0) REVERT: A 123 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8502 (mt-10) REVERT: A 320 MET cc_start: 0.7484 (ptp) cc_final: 0.7153 (ptp) REVERT: A 322 ASN cc_start: 0.6787 (t0) cc_final: 0.6499 (t0) REVERT: B 67 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8437 (tp30) REVERT: B 77 ILE cc_start: 0.9214 (mm) cc_final: 0.9001 (mp) REVERT: B 86 ASP cc_start: 0.9075 (t0) cc_final: 0.8607 (t0) REVERT: B 114 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7133 (tm-30) REVERT: C 123 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8432 (mt-10) REVERT: C 260 MET cc_start: 0.9238 (mtp) cc_final: 0.8866 (mtp) REVERT: C 320 MET cc_start: 0.7714 (ptp) cc_final: 0.7486 (ptm) REVERT: C 322 ASN cc_start: 0.6953 (t0) cc_final: 0.6750 (t0) REVERT: D 67 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8470 (tp30) REVERT: D 115 MET cc_start: 0.4701 (mtt) cc_final: 0.4359 (mtt) REVERT: F 67 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8350 (tp30) REVERT: F 76 ARG cc_start: 0.9154 (mtp180) cc_final: 0.8907 (mtp85) REVERT: F 86 ASP cc_start: 0.9165 (t0) cc_final: 0.8753 (t0) REVERT: F 105 GLN cc_start: 0.8969 (tp40) cc_final: 0.8557 (tp40) REVERT: G 113 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.7047 (mmm160) REVERT: G 128 GLU cc_start: 0.7626 (pm20) cc_final: 0.7225 (pm20) REVERT: G 153 TRP cc_start: 0.5440 (m100) cc_final: 0.5024 (m100) REVERT: H 87 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8066 (mtm180) REVERT: H 89 ASP cc_start: 0.8953 (p0) cc_final: 0.8296 (p0) REVERT: H 90 ASP cc_start: 0.8958 (m-30) cc_final: 0.8365 (m-30) REVERT: H 148 LEU cc_start: 0.8630 (tp) cc_final: 0.8274 (tp) REVERT: H 205 ILE cc_start: 0.7397 (mp) cc_final: 0.6913 (mp) REVERT: H 210 HIS cc_start: 0.7549 (t-170) cc_final: 0.6920 (t70) REVERT: I 87 ASP cc_start: 0.8526 (t0) cc_final: 0.8173 (t0) REVERT: I 128 GLU cc_start: 0.8377 (pm20) cc_final: 0.8085 (pm20) REVERT: I 141 LEU cc_start: 0.8097 (mp) cc_final: 0.7835 (tp) REVERT: I 204 GLN cc_start: 0.8275 (mt0) cc_final: 0.7903 (mp10) REVERT: J 123 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (p) REVERT: J 148 LEU cc_start: 0.8530 (mt) cc_final: 0.8195 (tp) REVERT: J 164 TRP cc_start: 0.7806 (m100) cc_final: 0.7420 (m100) REVERT: J 205 ILE cc_start: 0.7298 (mp) cc_final: 0.6574 (mp) REVERT: K 107 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8429 (mtmm) REVERT: K 108 LEU cc_start: 0.9121 (mp) cc_final: 0.8697 (tt) REVERT: K 141 LEU cc_start: 0.8264 (mp) cc_final: 0.7658 (tp) REVERT: L 46 GLU cc_start: 0.8474 (tt0) cc_final: 0.8222 (pt0) REVERT: L 132 PHE cc_start: 0.8012 (m-80) cc_final: 0.7670 (m-10) REVERT: L 164 TRP cc_start: 0.7698 (m100) cc_final: 0.6824 (m100) REVERT: L 179 VAL cc_start: 0.8767 (t) cc_final: 0.8460 (p) outliers start: 45 outliers final: 35 residues processed: 321 average time/residue: 0.1408 time to fit residues: 69.9026 Evaluate side-chains 311 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 114 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 94 optimal weight: 0.1980 chunk 134 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 322 ASN G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN K 39 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.090640 restraints weight = 33785.033| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.14 r_work: 0.2742 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19509 Z= 0.140 Angle : 0.617 9.199 26619 Z= 0.301 Chirality : 0.046 0.360 3153 Planarity : 0.004 0.037 3309 Dihedral : 4.592 24.388 2556 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.25 % Allowed : 13.60 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2352 helix: 2.89 (0.31), residues: 282 sheet: -0.12 (0.18), residues: 765 loop : -0.59 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.015 0.001 TYR I 145 PHE 0.011 0.001 PHE J 132 TRP 0.029 0.001 TRP H 164 HIS 0.019 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (19434) covalent geometry : angle 0.59381 / 0.30 (26418) SS BOND : bond 0.00409 / 0.32 ( 24) SS BOND : angle 1.71178 / 1.29 ( 48) hydrogen bonds : bond 0.02766 / 1.87 ( 731) hydrogen bonds : angle 5.19746 / 3.68 ( 1944) link_ALPHA1-2 : bond 0.00327 / 0.16 ( 3) link_ALPHA1-2 : angle 1.38477 / 1.24 ( 9) link_ALPHA1-3 : bond 0.00199 / 0.15 ( 9) link_ALPHA1-3 : angle 2.30639 / 1.59 ( 27) link_ALPHA1-6 : bond 0.00419 / 0.31 ( 9) link_ALPHA1-6 : angle 1.79709 / 1.36 ( 27) link_BETA1-4 : bond 0.00347 / 0.27 ( 15) link_BETA1-4 : angle 1.50924 / 1.10 ( 45) link_NAG-ASN : bond 0.00650 / 0.50 ( 15) link_NAG-ASN : angle 2.63772 / 1.43 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.7288 (ptp) cc_final: 0.6956 (ptp) REVERT: A 322 ASN cc_start: 0.6580 (t0) cc_final: 0.6270 (t0) REVERT: B 67 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8152 (tp30) REVERT: B 86 ASP cc_start: 0.8789 (t0) cc_final: 0.8300 (t0) REVERT: B 114 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7129 (tm-30) REVERT: C 123 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8228 (mt-10) REVERT: C 260 MET cc_start: 0.9024 (mtp) cc_final: 0.8630 (mtp) REVERT: D 67 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8203 (tp30) REVERT: F 67 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8049 (tp30) REVERT: F 76 ARG cc_start: 0.9054 (mtp180) cc_final: 0.8835 (mtp85) REVERT: F 86 ASP cc_start: 0.8891 (t0) cc_final: 0.8470 (t0) REVERT: F 105 GLN cc_start: 0.8821 (tp40) cc_final: 0.8508 (tp40) REVERT: G 128 GLU cc_start: 0.7594 (pm20) cc_final: 0.7391 (pm20) REVERT: G 145 TYR cc_start: 0.6874 (t80) cc_final: 0.5636 (t80) REVERT: G 153 TRP cc_start: 0.5384 (m100) cc_final: 0.4944 (m100) REVERT: H 87 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7973 (mtm180) REVERT: H 89 ASP cc_start: 0.8835 (p0) cc_final: 0.8222 (p0) REVERT: I 87 ASP cc_start: 0.8359 (t0) cc_final: 0.7997 (t0) REVERT: I 141 LEU cc_start: 0.7970 (mp) cc_final: 0.7739 (tp) REVERT: I 204 GLN cc_start: 0.8263 (mt0) cc_final: 0.7931 (mp10) REVERT: I 212 LYS cc_start: 0.5886 (tppp) cc_final: 0.5496 (ttmt) REVERT: J 148 LEU cc_start: 0.8521 (mt) cc_final: 0.8223 (tp) REVERT: J 164 TRP cc_start: 0.7747 (m100) cc_final: 0.7421 (m100) REVERT: J 205 ILE cc_start: 0.7323 (mp) cc_final: 0.6561 (mp) REVERT: K 108 LEU cc_start: 0.9070 (mp) cc_final: 0.8634 (tt) REVERT: L 46 GLU cc_start: 0.8253 (tt0) cc_final: 0.7972 (pt0) REVERT: L 132 PHE cc_start: 0.8038 (m-80) cc_final: 0.7679 (m-10) REVERT: L 164 TRP cc_start: 0.7699 (m100) cc_final: 0.6870 (m100) outliers start: 47 outliers final: 35 residues processed: 306 average time/residue: 0.1320 time to fit residues: 62.7189 Evaluate side-chains 313 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 60 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 ASN I 157 ASN K 39 GLN ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.086564 restraints weight = 33795.332| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.12 r_work: 0.2718 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19509 Z= 0.225 Angle : 0.658 9.215 26619 Z= 0.322 Chirality : 0.047 0.361 3153 Planarity : 0.004 0.041 3309 Dihedral : 4.661 23.807 2556 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.63 % Allowed : 14.13 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2352 helix: 2.79 (0.31), residues: 282 sheet: -0.28 (0.19), residues: 750 loop : -0.65 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 63 TYR 0.014 0.002 TYR F 94 PHE 0.014 0.002 PHE E 87 TRP 0.051 0.002 TRP H 164 HIS 0.019 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (19434) covalent geometry : angle 0.63438 / 0.32 (26418) SS BOND : bond 0.00553 / 0.43 ( 24) SS BOND : angle 1.84298 / 1.40 ( 48) hydrogen bonds : bond 0.02957 / 2.00 ( 731) hydrogen bonds : angle 5.24443 / 3.70 ( 1944) link_ALPHA1-2 : bond 0.00229 / 0.12 ( 3) link_ALPHA1-2 : angle 1.47043 / 1.31 ( 9) link_ALPHA1-3 : bond 0.00155 / 0.11 ( 9) link_ALPHA1-3 : angle 2.31738 / 1.61 ( 27) link_ALPHA1-6 : bond 0.00450 / 0.33 ( 9) link_ALPHA1-6 : angle 1.91013 / 1.44 ( 27) link_BETA1-4 : bond 0.00317 / 0.25 ( 15) link_BETA1-4 : angle 1.64236 / 1.17 ( 45) link_NAG-ASN : bond 0.00671 / 0.52 ( 15) link_NAG-ASN : angle 2.77834 / 1.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8130 (tt0) cc_final: 0.7353 (tt0) REVERT: A 123 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8353 (mt-10) REVERT: A 320 MET cc_start: 0.7357 (ptp) cc_final: 0.6963 (ptp) REVERT: A 322 ASN cc_start: 0.7046 (t0) cc_final: 0.6751 (t0) REVERT: B 67 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8205 (tp30) REVERT: B 86 ASP cc_start: 0.8825 (t0) cc_final: 0.8345 (t0) REVERT: B 114 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6949 (tm-30) REVERT: C 195 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: C 260 MET cc_start: 0.9060 (mtp) cc_final: 0.8677 (mtp) REVERT: D 67 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8248 (tp30) REVERT: D 115 MET cc_start: 0.4593 (OUTLIER) cc_final: 0.4375 (mtt) REVERT: E 35 GLU cc_start: 0.8186 (tp30) cc_final: 0.7947 (tp30) REVERT: F 67 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8131 (tp30) REVERT: F 76 ARG cc_start: 0.9087 (mtp180) cc_final: 0.8835 (mtp85) REVERT: F 86 ASP cc_start: 0.8926 (t0) cc_final: 0.8480 (t0) REVERT: F 105 GLN cc_start: 0.8954 (tp40) cc_final: 0.8650 (tp40) REVERT: G 153 TRP cc_start: 0.5426 (m100) cc_final: 0.4984 (m100) REVERT: H 87 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7956 (mtm180) REVERT: H 89 ASP cc_start: 0.8794 (p0) cc_final: 0.8230 (p0) REVERT: H 148 LEU cc_start: 0.8688 (tp) cc_final: 0.8383 (tp) REVERT: I 87 ASP cc_start: 0.8415 (t0) cc_final: 0.8058 (t0) REVERT: I 128 GLU cc_start: 0.8336 (pm20) cc_final: 0.8114 (pm20) REVERT: I 141 LEU cc_start: 0.8054 (mp) cc_final: 0.7772 (tp) REVERT: I 204 GLN cc_start: 0.8334 (mt0) cc_final: 0.7972 (mp10) REVERT: I 212 LYS cc_start: 0.5772 (tppp) cc_final: 0.5367 (ttmt) REVERT: J 148 LEU cc_start: 0.8482 (mt) cc_final: 0.8189 (tp) REVERT: J 164 TRP cc_start: 0.7814 (m100) cc_final: 0.7389 (m100) REVERT: J 205 ILE cc_start: 0.7259 (mp) cc_final: 0.6535 (mp) REVERT: K 108 LEU cc_start: 0.9028 (mp) cc_final: 0.8529 (tt) REVERT: L 46 GLU cc_start: 0.8272 (tt0) cc_final: 0.8018 (pt0) REVERT: L 132 PHE cc_start: 0.8047 (m-80) cc_final: 0.7776 (m-10) REVERT: L 164 TRP cc_start: 0.7810 (m100) cc_final: 0.6814 (m100) outliers start: 55 outliers final: 44 residues processed: 305 average time/residue: 0.1361 time to fit residues: 64.9688 Evaluate side-chains 313 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 132 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 210 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.089164 restraints weight = 33757.705| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.12 r_work: 0.2743 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19509 Z= 0.149 Angle : 0.628 10.634 26619 Z= 0.307 Chirality : 0.046 0.349 3153 Planarity : 0.004 0.037 3309 Dihedral : 4.553 23.597 2556 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.35 % Allowed : 14.80 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2352 helix: 2.86 (0.31), residues: 282 sheet: -0.11 (0.19), residues: 732 loop : -0.69 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 63 TYR 0.016 0.001 TYR G 145 PHE 0.011 0.001 PHE J 132 TRP 0.068 0.002 TRP H 164 HIS 0.015 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (19434) covalent geometry : angle 0.60574 / 0.30 (26418) SS BOND : bond 0.00377 / 0.29 ( 24) SS BOND : angle 1.71507 / 1.28 ( 48) hydrogen bonds : bond 0.02756 / 1.86 ( 731) hydrogen bonds : angle 5.12487 / 3.61 ( 1944) link_ALPHA1-2 : bond 0.00330 / 0.17 ( 3) link_ALPHA1-2 : angle 1.37368 / 1.23 ( 9) link_ALPHA1-3 : bond 0.00208 / 0.16 ( 9) link_ALPHA1-3 : angle 2.28795 / 1.58 ( 27) link_ALPHA1-6 : bond 0.00389 / 0.29 ( 9) link_ALPHA1-6 : angle 1.78496 / 1.35 ( 27) link_BETA1-4 : bond 0.00323 / 0.26 ( 15) link_BETA1-4 : angle 1.48422 / 1.07 ( 45) link_NAG-ASN : bond 0.00653 / 0.50 ( 15) link_NAG-ASN : angle 2.73038 / 1.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8408 (mt-10) REVERT: A 320 MET cc_start: 0.7299 (ptp) cc_final: 0.6917 (ptp) REVERT: B 67 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8181 (tp30) REVERT: B 86 ASP cc_start: 0.8792 (t0) cc_final: 0.8268 (t0) REVERT: B 114 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7061 (tm-30) REVERT: C 195 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.6971 (m-80) REVERT: C 260 MET cc_start: 0.9038 (mtp) cc_final: 0.8656 (mtp) REVERT: C 262 THR cc_start: 0.8805 (m) cc_final: 0.8511 (t) REVERT: D 67 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8171 (tp30) REVERT: D 115 MET cc_start: 0.4603 (OUTLIER) cc_final: 0.4381 (mtt) REVERT: F 67 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8061 (tp30) REVERT: F 76 ARG cc_start: 0.9054 (mtp180) cc_final: 0.8829 (mtp85) REVERT: F 86 ASP cc_start: 0.8910 (t0) cc_final: 0.8553 (t0) REVERT: F 105 GLN cc_start: 0.8930 (tp40) cc_final: 0.8578 (tp40) REVERT: G 128 GLU cc_start: 0.7701 (pm20) cc_final: 0.7431 (pm20) REVERT: G 153 TRP cc_start: 0.5373 (m100) cc_final: 0.5000 (m100) REVERT: G 204 GLN cc_start: 0.7714 (pp30) cc_final: 0.7465 (pp30) REVERT: H 87 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7931 (mtm180) REVERT: H 89 ASP cc_start: 0.8789 (p0) cc_final: 0.8226 (p0) REVERT: H 148 LEU cc_start: 0.8649 (tp) cc_final: 0.8293 (tp) REVERT: I 87 ASP cc_start: 0.8384 (t0) cc_final: 0.8007 (t0) REVERT: I 204 GLN cc_start: 0.8257 (mt0) cc_final: 0.7913 (mp10) REVERT: I 212 LYS cc_start: 0.5897 (tppp) cc_final: 0.5550 (ttmt) REVERT: J 148 LEU cc_start: 0.8446 (mt) cc_final: 0.8150 (tp) REVERT: J 164 TRP cc_start: 0.7774 (m100) cc_final: 0.7291 (m100) REVERT: J 205 ILE cc_start: 0.7250 (mp) cc_final: 0.6526 (mp) REVERT: K 108 LEU cc_start: 0.9046 (mp) cc_final: 0.8586 (tt) REVERT: L 46 GLU cc_start: 0.8257 (tt0) cc_final: 0.8018 (pt0) REVERT: L 164 TRP cc_start: 0.7694 (m100) cc_final: 0.6722 (m100) outliers start: 49 outliers final: 43 residues processed: 298 average time/residue: 0.1360 time to fit residues: 63.9135 Evaluate side-chains 307 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 145 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 192 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 164 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091011 restraints weight = 33435.844| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.99 r_work: 0.2757 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19509 Z= 0.137 Angle : 0.619 9.320 26619 Z= 0.304 Chirality : 0.046 0.349 3153 Planarity : 0.004 0.040 3309 Dihedral : 4.475 23.422 2556 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.54 % Allowed : 15.18 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2352 helix: 2.93 (0.30), residues: 282 sheet: -0.04 (0.18), residues: 768 loop : -0.68 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 63 TYR 0.024 0.001 TYR G 145 PHE 0.015 0.001 PHE L 132 TRP 0.065 0.001 TRP H 164 HIS 0.022 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (19434) covalent geometry : angle 0.59598 / 0.30 (26418) SS BOND : bond 0.00369 / 0.30 ( 24) SS BOND : angle 1.68990 / 1.26 ( 48) hydrogen bonds : bond 0.02704 / 1.83 ( 731) hydrogen bonds : angle 5.06448 / 3.57 ( 1944) link_ALPHA1-2 : bond 0.00356 / 0.18 ( 3) link_ALPHA1-2 : angle 1.37036 / 1.22 ( 9) link_ALPHA1-3 : bond 0.00249 / 0.18 ( 9) link_ALPHA1-3 : angle 2.26510 / 1.56 ( 27) link_ALPHA1-6 : bond 0.00365 / 0.27 ( 9) link_ALPHA1-6 : angle 1.76031 / 1.33 ( 27) link_BETA1-4 : bond 0.00336 / 0.27 ( 15) link_BETA1-4 : angle 1.43638 / 1.05 ( 45) link_NAG-ASN : bond 0.00625 / 0.49 ( 15) link_NAG-ASN : angle 2.71468 / 1.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8425 (mt-10) REVERT: A 320 MET cc_start: 0.7264 (ptp) cc_final: 0.6887 (ptp) REVERT: B 67 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8147 (tp30) REVERT: B 114 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7071 (tm-30) REVERT: C 35 GLU cc_start: 0.7826 (tp30) cc_final: 0.7585 (tp30) REVERT: C 195 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: C 260 MET cc_start: 0.9018 (mtp) cc_final: 0.8634 (mtp) REVERT: C 262 THR cc_start: 0.8769 (m) cc_final: 0.8448 (t) REVERT: C 320 MET cc_start: 0.7645 (ptp) cc_final: 0.7355 (ptp) REVERT: D 67 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8160 (tp30) REVERT: F 67 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8099 (tp30) REVERT: F 76 ARG cc_start: 0.9039 (mtp180) cc_final: 0.8820 (mtp85) REVERT: F 86 ASP cc_start: 0.8882 (t0) cc_final: 0.8457 (t0) REVERT: F 105 GLN cc_start: 0.8924 (tp40) cc_final: 0.8592 (tp40) REVERT: G 128 GLU cc_start: 0.7724 (pm20) cc_final: 0.7519 (pm20) REVERT: G 153 TRP cc_start: 0.5337 (m100) cc_final: 0.4969 (m100) REVERT: H 87 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7916 (mtm180) REVERT: H 89 ASP cc_start: 0.8811 (p0) cc_final: 0.8241 (p0) REVERT: H 126 SER cc_start: 0.8022 (m) cc_final: 0.7382 (t) REVERT: H 148 LEU cc_start: 0.8549 (tp) cc_final: 0.8131 (tp) REVERT: I 87 ASP cc_start: 0.8373 (t0) cc_final: 0.7986 (t0) REVERT: I 128 GLU cc_start: 0.7893 (pm20) cc_final: 0.7666 (pm20) REVERT: I 204 GLN cc_start: 0.8290 (mt0) cc_final: 0.8007 (mp10) REVERT: I 212 LYS cc_start: 0.5871 (tppp) cc_final: 0.5537 (ttmt) REVERT: J 148 LEU cc_start: 0.8412 (mt) cc_final: 0.8127 (tp) REVERT: J 164 TRP cc_start: 0.7700 (m100) cc_final: 0.6919 (m100) REVERT: J 205 ILE cc_start: 0.7373 (mp) cc_final: 0.6748 (mp) REVERT: K 108 LEU cc_start: 0.9043 (mp) cc_final: 0.8576 (tt) REVERT: L 46 GLU cc_start: 0.8246 (tt0) cc_final: 0.8005 (pt0) REVERT: L 132 PHE cc_start: 0.7713 (m-10) cc_final: 0.7215 (m-80) REVERT: L 164 TRP cc_start: 0.7681 (m100) cc_final: 0.6675 (m100) outliers start: 53 outliers final: 46 residues processed: 305 average time/residue: 0.1269 time to fit residues: 61.4141 Evaluate side-chains 310 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 129 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 92 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.088271 restraints weight = 33688.371| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.20 r_work: 0.2723 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19509 Z= 0.222 Angle : 0.663 9.394 26619 Z= 0.326 Chirality : 0.047 0.356 3153 Planarity : 0.004 0.041 3309 Dihedral : 4.579 22.604 2556 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.44 % Allowed : 15.57 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2352 helix: 2.84 (0.30), residues: 279 sheet: -0.12 (0.18), residues: 774 loop : -0.72 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 63 TYR 0.021 0.002 TYR C 257 PHE 0.015 0.002 PHE E 87 TRP 0.062 0.002 TRP H 164 HIS 0.012 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (19434) covalent geometry : angle 0.63941 / 0.32 (26418) SS BOND : bond 0.00765 / 0.64 ( 24) SS BOND : angle 1.95055 / 1.45 ( 48) hydrogen bonds : bond 0.02927 / 1.96 ( 731) hydrogen bonds : angle 5.14082 / 3.62 ( 1944) link_ALPHA1-2 : bond 0.00259 / 0.13 ( 3) link_ALPHA1-2 : angle 1.47057 / 1.31 ( 9) link_ALPHA1-3 : bond 0.00186 / 0.14 ( 9) link_ALPHA1-3 : angle 2.28182 / 1.58 ( 27) link_ALPHA1-6 : bond 0.00379 / 0.28 ( 9) link_ALPHA1-6 : angle 1.87406 / 1.41 ( 27) link_BETA1-4 : bond 0.00308 / 0.25 ( 15) link_BETA1-4 : angle 1.58136 / 1.13 ( 45) link_NAG-ASN : bond 0.00666 / 0.52 ( 15) link_NAG-ASN : angle 2.80401 / 1.53 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.7438 (ptp) cc_final: 0.7040 (ptp) REVERT: B 67 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8151 (tp30) REVERT: B 85 GLU cc_start: 0.8887 (tp30) cc_final: 0.8584 (tp30) REVERT: B 86 ASP cc_start: 0.8791 (t0) cc_final: 0.8278 (t0) REVERT: B 114 GLU cc_start: 0.7753 (mm-30) cc_final: 0.6998 (tm-30) REVERT: C 195 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: C 260 MET cc_start: 0.9055 (mtp) cc_final: 0.8680 (mtp) REVERT: D 67 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8208 (tp30) REVERT: F 67 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8148 (tp30) REVERT: F 76 ARG cc_start: 0.9082 (mtp180) cc_final: 0.8829 (mtp85) REVERT: F 86 ASP cc_start: 0.8901 (t0) cc_final: 0.8417 (t0) REVERT: F 105 GLN cc_start: 0.9012 (tp40) cc_final: 0.8676 (tp40) REVERT: G 128 GLU cc_start: 0.7736 (pm20) cc_final: 0.7512 (pm20) REVERT: G 153 TRP cc_start: 0.5392 (m100) cc_final: 0.5035 (m100) REVERT: H 87 ARG cc_start: 0.8284 (mtm180) cc_final: 0.7938 (mtm180) REVERT: H 89 ASP cc_start: 0.8778 (p0) cc_final: 0.8199 (p0) REVERT: H 148 LEU cc_start: 0.8558 (tp) cc_final: 0.8161 (tp) REVERT: I 87 ASP cc_start: 0.8411 (t0) cc_final: 0.8030 (t0) REVERT: I 128 GLU cc_start: 0.7891 (pm20) cc_final: 0.7624 (pm20) REVERT: I 204 GLN cc_start: 0.8403 (mt0) cc_final: 0.8188 (mp10) REVERT: I 212 LYS cc_start: 0.5777 (tppp) cc_final: 0.5426 (ttmt) REVERT: J 148 LEU cc_start: 0.8409 (mt) cc_final: 0.8126 (tp) REVERT: J 164 TRP cc_start: 0.7685 (m100) cc_final: 0.6676 (m100) REVERT: J 205 ILE cc_start: 0.7491 (mp) cc_final: 0.6868 (mp) REVERT: K 108 LEU cc_start: 0.9036 (mp) cc_final: 0.8502 (tt) REVERT: L 46 GLU cc_start: 0.8308 (tt0) cc_final: 0.8068 (pt0) REVERT: L 132 PHE cc_start: 0.7803 (m-10) cc_final: 0.7217 (m-80) REVERT: L 164 TRP cc_start: 0.7664 (m100) cc_final: 0.6634 (m100) outliers start: 51 outliers final: 48 residues processed: 293 average time/residue: 0.1264 time to fit residues: 58.4083 Evaluate side-chains 304 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 136 SER Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 27 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS K 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.085706 restraints weight = 34160.950| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.57 r_work: 0.2771 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19509 Z= 0.139 Angle : 0.630 12.254 26619 Z= 0.309 Chirality : 0.046 0.351 3153 Planarity : 0.004 0.037 3309 Dihedral : 4.495 23.569 2556 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.20 % Allowed : 15.95 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2352 helix: 2.93 (0.31), residues: 279 sheet: -0.05 (0.18), residues: 768 loop : -0.72 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 63 TYR 0.023 0.001 TYR C 257 PHE 0.024 0.001 PHE G 144 TRP 0.061 0.002 TRP H 164 HIS 0.015 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (19434) covalent geometry : angle 0.60661 / 0.30 (26418) SS BOND : bond 0.00381 / 0.31 ( 24) SS BOND : angle 1.84016 / 1.35 ( 48) hydrogen bonds : bond 0.02717 / 1.83 ( 731) hydrogen bonds : angle 5.06820 / 3.57 ( 1944) link_ALPHA1-2 : bond 0.00366 / 0.18 ( 3) link_ALPHA1-2 : angle 1.36618 / 1.22 ( 9) link_ALPHA1-3 : bond 0.00272 / 0.20 ( 9) link_ALPHA1-3 : angle 2.26165 / 1.56 ( 27) link_ALPHA1-6 : bond 0.00341 / 0.25 ( 9) link_ALPHA1-6 : angle 1.74402 / 1.31 ( 27) link_BETA1-4 : bond 0.00339 / 0.27 ( 15) link_BETA1-4 : angle 1.42522 / 1.03 ( 45) link_NAG-ASN : bond 0.00647 / 0.50 ( 15) link_NAG-ASN : angle 2.74333 / 1.48 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8383 (tp30) REVERT: B 85 GLU cc_start: 0.9073 (tp30) cc_final: 0.8827 (tp30) REVERT: B 86 ASP cc_start: 0.9021 (t0) cc_final: 0.8482 (t0) REVERT: B 114 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7003 (tm-30) REVERT: C 195 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.6870 (m-80) REVERT: C 260 MET cc_start: 0.9240 (mtp) cc_final: 0.8882 (mtp) REVERT: C 262 THR cc_start: 0.8946 (m) cc_final: 0.8583 (t) REVERT: C 320 MET cc_start: 0.7444 (ptp) cc_final: 0.7110 (ptm) REVERT: D 67 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8466 (tp30) REVERT: D 85 GLU cc_start: 0.8997 (tp30) cc_final: 0.8771 (tp30) REVERT: F 67 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8340 (tp30) REVERT: F 76 ARG cc_start: 0.9111 (mtp180) cc_final: 0.8874 (mtp85) REVERT: F 86 ASP cc_start: 0.9172 (t0) cc_final: 0.8750 (t0) REVERT: F 105 GLN cc_start: 0.9016 (tp40) cc_final: 0.8683 (tp40) REVERT: G 128 GLU cc_start: 0.7766 (pm20) cc_final: 0.7544 (pm20) REVERT: G 153 TRP cc_start: 0.5419 (m100) cc_final: 0.5055 (m100) REVERT: H 87 ARG cc_start: 0.8367 (mtm180) cc_final: 0.8068 (mtm180) REVERT: H 89 ASP cc_start: 0.8904 (p0) cc_final: 0.8378 (p0) REVERT: H 126 SER cc_start: 0.8125 (m) cc_final: 0.7502 (t) REVERT: H 148 LEU cc_start: 0.8525 (tp) cc_final: 0.8127 (tp) REVERT: I 87 ASP cc_start: 0.8499 (t0) cc_final: 0.8097 (t0) REVERT: I 128 GLU cc_start: 0.7888 (pm20) cc_final: 0.7603 (pm20) REVERT: I 204 GLN cc_start: 0.8454 (mt0) cc_final: 0.8198 (mp10) REVERT: I 212 LYS cc_start: 0.5897 (tppp) cc_final: 0.5571 (ttmt) REVERT: J 148 LEU cc_start: 0.8654 (mt) cc_final: 0.8394 (tp) REVERT: J 164 TRP cc_start: 0.7666 (m100) cc_final: 0.6752 (m100) REVERT: J 205 ILE cc_start: 0.7435 (mp) cc_final: 0.6859 (mp) REVERT: K 108 LEU cc_start: 0.9124 (mp) cc_final: 0.8596 (tt) REVERT: K 141 LEU cc_start: 0.8181 (mp) cc_final: 0.7617 (tp) REVERT: L 46 GLU cc_start: 0.8531 (tt0) cc_final: 0.8270 (pt0) REVERT: L 132 PHE cc_start: 0.7795 (m-10) cc_final: 0.7231 (m-80) REVERT: L 164 TRP cc_start: 0.7684 (m100) cc_final: 0.6629 (m100) outliers start: 46 outliers final: 43 residues processed: 297 average time/residue: 0.1306 time to fit residues: 61.3075 Evaluate side-chains 301 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain L residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 75 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 GLN G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS K 39 GLN ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.078139 restraints weight = 34123.863| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.52 r_work: 0.2738 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19509 Z= 0.242 Angle : 0.679 11.369 26619 Z= 0.334 Chirality : 0.048 0.359 3153 Planarity : 0.004 0.039 3309 Dihedral : 4.631 23.821 2556 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.49 % Allowed : 16.24 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2352 helix: 2.77 (0.31), residues: 279 sheet: -0.08 (0.19), residues: 765 loop : -0.79 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 63 TYR 0.022 0.002 TYR C 257 PHE 0.015 0.002 PHE E 87 TRP 0.062 0.002 TRP H 164 HIS 0.016 0.002 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (19434) covalent geometry : angle 0.65520 / 0.33 (26418) SS BOND : bond 0.00538 / 0.44 ( 24) SS BOND : angle 2.06805 / 1.52 ( 48) hydrogen bonds : bond 0.03018 / 2.02 ( 731) hydrogen bonds : angle 5.18162 / 3.65 ( 1944) link_ALPHA1-2 : bond 0.00246 / 0.12 ( 3) link_ALPHA1-2 : angle 1.49857 / 1.33 ( 9) link_ALPHA1-3 : bond 0.00194 / 0.15 ( 9) link_ALPHA1-3 : angle 2.26561 / 1.57 ( 27) link_ALPHA1-6 : bond 0.00364 / 0.27 ( 9) link_ALPHA1-6 : angle 1.90519 / 1.43 ( 27) link_BETA1-4 : bond 0.00307 / 0.25 ( 15) link_BETA1-4 : angle 1.59816 / 1.13 ( 45) link_NAG-ASN : bond 0.00692 / 0.54 ( 15) link_NAG-ASN : angle 2.82333 / 1.55 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5277.47 seconds wall clock time: 91 minutes 27.54 seconds (5487.54 seconds total)