Starting phenix.real_space_refine on Sat Jul 4 15:18:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k39_22653/07_2026/7k39_22653.cif" } resolution = 3.0 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= 0.009 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 99 5.16 5 C 13452 2.51 5 N 3639 2.21 5 O 4371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 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: 21561 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.36, per 1000 atoms: 0.25 Number of scatterers: 21561 At special positions: 0 Unit cell: (184.87, 184.87, 146.3, 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 99 16.00 O 4371 8.00 N 3639 7.00 C 13452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.09 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.02 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.16 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.02 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.90 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 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=2.03 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 B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG F 301 " - " ASN F 154 " " 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: 1.78 Conformation dependent library (CDL) restraints added in 857.0 milliseconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4962 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 63 sheets defined 19.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.312A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (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 38 through 50 removed outlier: 4.422A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.312A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (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 38 through 50 removed outlier: 4.423A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.312A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (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 38 through 50 removed outlier: 4.423A pdb=" N GLY F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 172 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: 3.670A 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 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.660A pdb=" N THR H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.592A 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 Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 197 through 202 removed outlier: 3.661A 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: 3.728A pdb=" N LEU K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 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 Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 197 through 202 removed outlier: 3.660A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 4.766A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.983A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.531A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.217A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.766A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.983A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.883A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.531A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.217A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 37 removed outlier: 4.766A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.983A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.884A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.884A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.531A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.218A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.521A pdb=" N THR G 109 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 17 through 22 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 4.016A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.167A 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: 4.175A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.541A 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: 6.697A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.697A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.130A 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: 6.033A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER H 189 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL H 191 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR H 175 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR H 193 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL H 173 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 160 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.865A pdb=" N THR I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.443A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.713A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.800A 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 154 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: 6.697A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.697A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.129A 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: 6.033A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER J 189 " --> pdb=" O PRO J 177 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL J 191 " --> pdb=" O THR J 175 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR J 175 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR J 193 " --> pdb=" O VAL J 173 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL J 173 " --> pdb=" O THR J 193 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 160 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.678A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.481A 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: 3.650A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.737A 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 159 removed outlier: 3.519A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (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: 6.698A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.698A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.129A 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: 6.033A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER L 189 " --> pdb=" O PRO L 177 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL L 191 " --> pdb=" O THR L 175 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR L 175 " --> pdb=" O VAL L 191 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR L 193 " --> pdb=" O VAL L 173 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL L 173 " --> pdb=" O THR L 193 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 160 through 164 914 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.36 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: 6927 1.34 - 1.46: 5129 1.46 - 1.58: 9814 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 22008 Sorted by residual: bond pdb=" C3 MAN R 4 " pdb=" O3 MAN R 4 " ideal model delta sigma weight residual 1.408 1.446 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 1.408 1.446 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C3 MAN O 4 " pdb=" O3 MAN O 4 " ideal model delta sigma weight residual 1.408 1.445 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 22003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 28831 1.83 - 3.65: 847 3.65 - 5.48: 165 5.48 - 7.31: 37 7.31 - 9.14: 6 Bond angle restraints: 29886 Sorted by residual: angle pdb=" N GLN G 6 " pdb=" CA GLN G 6 " pdb=" C GLN G 6 " ideal model delta sigma weight residual 108.22 112.26 -4.04 9.00e-01 1.23e+00 2.02e+01 angle pdb=" N LYS G 195 " pdb=" CA LYS G 195 " pdb=" CB LYS G 195 " ideal model delta sigma weight residual 114.17 110.11 4.06 1.14e+00 7.69e-01 1.27e+01 angle pdb=" N TYR L 54 " pdb=" CA TYR L 54 " pdb=" CB TYR L 54 " ideal model delta sigma weight residual 114.17 110.13 4.04 1.14e+00 7.69e-01 1.26e+01 angle pdb=" N LEU D 52 " pdb=" CA LEU D 52 " pdb=" C LEU D 52 " ideal model delta sigma weight residual 114.56 110.08 4.48 1.27e+00 6.20e-01 1.24e+01 angle pdb=" N TYR H 54 " pdb=" CA TYR H 54 " pdb=" CB TYR H 54 " ideal model delta sigma weight residual 114.17 110.16 4.01 1.14e+00 7.69e-01 1.24e+01 ... (remaining 29881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 11597 17.39 - 34.77: 981 34.77 - 52.16: 138 52.16 - 69.54: 35 69.54 - 86.93: 14 Dihedral angle restraints: 12765 sinusoidal: 5007 harmonic: 7758 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 32.50 60.50 1 1.00e+01 1.00e-02 4.87e+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 38.48 54.52 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CA CYS E 14 " pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " ideal model delta sinusoidal sigma weight residual 79.00 3.02 75.98 1 2.00e+01 2.50e-03 1.82e+01 ... (remaining 12762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2921 0.069 - 0.137: 525 0.137 - 0.206: 46 0.206 - 0.275: 6 0.275 - 0.343: 9 Chirality restraints: 3507 Sorted by residual: chirality pdb=" C3 MAN O 4 " pdb=" C2 MAN O 4 " pdb=" C4 MAN O 4 " pdb=" O3 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" C4 MAN U 4 " pdb=" O3 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" C4 MAN R 4 " pdb=" O3 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 3504 not shown) Planarity restraints: 3795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 3 " -0.007 2.00e-02 2.50e+03 1.14e-02 2.28e+00 pdb=" CG PHE F 3 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE F 3 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE F 3 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE F 3 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 3 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 3 " -0.007 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE D 3 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE D 3 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 3 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 3 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 3 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA I 13 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO I 14 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.021 5.00e-02 4.00e+02 ... (remaining 3792 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 382 2.66 - 3.22: 19898 3.22 - 3.78: 33617 3.78 - 4.34: 47755 4.34 - 4.90: 79170 Nonbonded interactions: 180822 Sorted by model distance: nonbonded pdb=" OE1 GLU B 74 " pdb=" NE2 GLN B 78 " model vdw 2.099 3.120 nonbonded pdb=" OE1 GLU D 74 " pdb=" NE2 GLN D 78 " model vdw 2.099 3.120 nonbonded pdb=" OE1 GLU F 74 " pdb=" NE2 GLN F 78 " model vdw 2.100 3.120 nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.103 3.040 nonbonded pdb=" O SER G 92 " pdb=" OG SER G 100 " model vdw 2.105 3.040 ... (remaining 180817 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: 0.04 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: 2.500 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.280 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 0.133 22092 Z= 0.336 Angle : 0.813 11.841 30108 Z= 0.411 Chirality : 0.054 0.343 3507 Planarity : 0.004 0.037 3777 Dihedral : 12.896 86.928 7713 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.61 (0.16), residues: 2670 helix: 2.05 (0.25), residues: 363 sheet: -0.31 (0.17), residues: 834 loop : -1.10 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 17 TYR 0.018 0.002 TYR I 178 PHE 0.024 0.002 PHE F 3 TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.33 (22008) covalent geometry : angle 0.78359 / 0.40 (29886) SS BOND : bond 0.03604 / 2.14 ( 30) SS BOND : angle 2.18695 / 1.22 ( 60) hydrogen bonds : bond 0.13969 / 9.48 ( 872) hydrogen bonds : angle 7.01230 / 4.91 ( 2319) link_ALPHA1-2 : bond 0.00214 / 0.11 ( 3) link_ALPHA1-2 : angle 2.04435 / 1.14 ( 9) link_ALPHA1-3 : bond 0.00323 / 0.16 ( 9) link_ALPHA1-3 : angle 3.69514 / 2.04 ( 27) link_ALPHA1-6 : bond 0.00520 / 0.34 ( 9) link_ALPHA1-6 : angle 2.68794 / 1.62 ( 27) link_BETA1-4 : bond 0.00437 / 0.27 ( 15) link_BETA1-4 : angle 1.76184 / 1.12 ( 45) link_NAG-ASN : bond 0.00755 / 0.48 ( 18) link_NAG-ASN : angle 3.09130 / 2.03 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.868 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 31 ASP cc_start: 0.7923 (m-30) cc_final: 0.7606 (m-30) REVERT: A 45 SER cc_start: 0.9230 (p) cc_final: 0.8876 (t) REVERT: A 189 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 190 GLU cc_start: 0.8549 (tt0) cc_final: 0.8349 (tt0) REVERT: A 268 MET cc_start: 0.9011 (ttm) cc_final: 0.8750 (ttm) REVERT: A 280 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7848 (tp30) REVERT: B 17 MET cc_start: 0.8411 (tpp) cc_final: 0.8132 (ttm) REVERT: B 76 ARG cc_start: 0.8565 (mtp180) cc_final: 0.8090 (mtt180) REVERT: C 35 GLU cc_start: 0.8078 (tt0) cc_final: 0.7596 (tt0) REVERT: C 77 ASP cc_start: 0.7971 (m-30) cc_final: 0.7628 (m-30) REVERT: C 173 ASN cc_start: 0.8174 (p0) cc_final: 0.7690 (t0) REVERT: C 307 LYS cc_start: 0.8435 (mttp) cc_final: 0.8223 (mmtt) REVERT: D 17 MET cc_start: 0.8310 (tpp) cc_final: 0.7632 (ttm) REVERT: D 32 THR cc_start: 0.8561 (m) cc_final: 0.8319 (p) REVERT: D 47 GLN cc_start: 0.9047 (mt0) cc_final: 0.8697 (mt0) REVERT: D 62 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8562 (mptm) REVERT: D 133 MET cc_start: 0.9006 (mtm) cc_final: 0.8747 (mtp) REVERT: D 150 GLU cc_start: 0.7269 (pp20) cc_final: 0.6417 (tm-30) REVERT: E 31 ASP cc_start: 0.7725 (m-30) cc_final: 0.7355 (m-30) REVERT: E 77 ASP cc_start: 0.8061 (m-30) cc_final: 0.7857 (m-30) REVERT: E 189 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8469 (tm130) REVERT: F 40 SER cc_start: 0.8687 (m) cc_final: 0.8222 (p) REVERT: F 47 GLN cc_start: 0.8804 (mt0) cc_final: 0.8408 (mt0) REVERT: F 82 LYS cc_start: 0.9038 (mttt) cc_final: 0.8716 (mttt) REVERT: F 105 GLN cc_start: 0.8643 (tp40) cc_final: 0.8368 (tp-100) REVERT: F 115 MET cc_start: 0.8892 (tpt) cc_final: 0.8496 (tpt) REVERT: F 133 MET cc_start: 0.8947 (mtm) cc_final: 0.8563 (mtm) REVERT: F 139 LYS cc_start: 0.8694 (tttp) cc_final: 0.8440 (ttmm) REVERT: F 150 GLU cc_start: 0.7307 (pp20) cc_final: 0.6715 (tp30) REVERT: G 81 GLN cc_start: 0.7257 (pm20) cc_final: 0.7030 (pm20) REVERT: G 201 VAL cc_start: 0.5634 (p) cc_final: 0.5413 (p) REVERT: H 13 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8820 (mmtp) REVERT: H 81 MET cc_start: 0.8996 (ttp) cc_final: 0.8576 (ttt) REVERT: H 87 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7816 (mtp85) REVERT: H 159 PRO cc_start: 0.6635 (Cg_exo) cc_final: 0.6429 (Cg_endo) REVERT: H 181 GLN cc_start: 0.7483 (tt0) cc_final: 0.6912 (mt0) REVERT: I 55 ASN cc_start: 0.7727 (t0) cc_final: 0.7270 (t0) REVERT: I 167 SER cc_start: 0.8256 (t) cc_final: 0.7766 (m) REVERT: J 59 LYS cc_start: 0.8898 (tptp) cc_final: 0.8460 (tppp) REVERT: J 106 MET cc_start: 0.8453 (mtm) cc_final: 0.8235 (mtm) REVERT: J 181 GLN cc_start: 0.7721 (tt0) cc_final: 0.6863 (mt0) REVERT: J 185 LEU cc_start: 0.8571 (mp) cc_final: 0.8075 (mt) REVERT: K 18 VAL cc_start: 0.7938 (t) cc_final: 0.7569 (p) REVERT: L 13 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8662 (mptm) REVERT: L 54 TYR cc_start: 0.8131 (t80) cc_final: 0.7896 (t80) REVERT: L 59 LYS cc_start: 0.8687 (tptp) cc_final: 0.8354 (tptm) REVERT: L 62 LYS cc_start: 0.8614 (tppt) cc_final: 0.8369 (tttp) REVERT: L 87 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7424 (mtp85) REVERT: L 181 GLN cc_start: 0.7635 (tt0) cc_final: 0.6522 (mt0) outliers start: 0 outliers final: 1 residues processed: 412 average time/residue: 0.7226 time to fit residues: 333.7386 Evaluate side-chains 275 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN B 12 ASN B 125 GLN C 191 GLN D 125 GLN E 191 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS I 40 GLN ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 36 HIS K 40 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 43 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101410 restraints weight = 30006.688| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.55 r_work: 0.2806 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22092 Z= 0.158 Angle : 0.661 9.373 30108 Z= 0.323 Chirality : 0.048 0.403 3507 Planarity : 0.004 0.039 3777 Dihedral : 4.950 25.793 2903 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.70 % Allowed : 8.56 % Favored : 88.75 % 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: -0.41 (0.16), residues: 2670 helix: 2.16 (0.26), residues: 381 sheet: -0.04 (0.18), residues: 801 loop : -1.07 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 113 TYR 0.019 0.002 TYR A 100 PHE 0.013 0.002 PHE F 9 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (22008) covalent geometry : angle 0.63869 / 0.32 (29886) SS BOND : bond 0.00586 / 0.35 ( 30) SS BOND : angle 1.23011 / 0.70 ( 60) hydrogen bonds : bond 0.03769 / 2.48 ( 872) hydrogen bonds : angle 5.72524 / 4.03 ( 2319) link_ALPHA1-2 : bond 0.00186 / 0.09 ( 3) link_ALPHA1-2 : angle 1.76150 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00335 / 0.19 ( 9) link_ALPHA1-3 : angle 2.78405 / 1.49 ( 27) link_ALPHA1-6 : bond 0.00446 / 0.27 ( 9) link_ALPHA1-6 : angle 1.92532 / 1.12 ( 27) link_BETA1-4 : bond 0.00258 / 0.17 ( 15) link_BETA1-4 : angle 1.68011 / 1.11 ( 45) link_NAG-ASN : bond 0.00715 / 0.41 ( 18) link_NAG-ASN : angle 2.69749 / 1.85 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 0.815 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 31 ASP cc_start: 0.8438 (m-30) cc_final: 0.8224 (m-30) REVERT: A 189 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8670 (tm-30) REVERT: A 280 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8569 (tp30) REVERT: B 121 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8709 (ttpt) REVERT: C 35 GLU cc_start: 0.8651 (tt0) cc_final: 0.8297 (tt0) REVERT: C 77 ASP cc_start: 0.8291 (m-30) cc_final: 0.7994 (m-30) REVERT: C 173 ASN cc_start: 0.8598 (p0) cc_final: 0.8063 (t0) REVERT: C 307 LYS cc_start: 0.8949 (mttp) cc_final: 0.8525 (mmtt) REVERT: D 17 MET cc_start: 0.8601 (tpp) cc_final: 0.7901 (ttm) REVERT: D 47 GLN cc_start: 0.9173 (mt0) cc_final: 0.8807 (mt0) REVERT: D 65 GLN cc_start: 0.9222 (mt0) cc_final: 0.8927 (mt0) REVERT: D 150 GLU cc_start: 0.7781 (pp20) cc_final: 0.6793 (tm-30) REVERT: E 31 ASP cc_start: 0.8443 (m-30) cc_final: 0.8102 (m-30) REVERT: E 40 THR cc_start: 0.9379 (t) cc_final: 0.9143 (p) REVERT: E 189 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8685 (tp40) REVERT: F 17 MET cc_start: 0.8758 (ttm) cc_final: 0.8414 (ttm) REVERT: F 47 GLN cc_start: 0.9021 (mt0) cc_final: 0.8623 (mt0) REVERT: F 115 MET cc_start: 0.9154 (tpt) cc_final: 0.8917 (tpt) REVERT: F 133 MET cc_start: 0.9262 (mtm) cc_final: 0.9031 (mtp) REVERT: F 150 GLU cc_start: 0.7851 (pp20) cc_final: 0.7118 (tp30) REVERT: G 16 GLN cc_start: 0.7055 (pm20) cc_final: 0.6757 (pm20) REVERT: H 81 MET cc_start: 0.9209 (ttp) cc_final: 0.8907 (ttt) REVERT: H 155 TYR cc_start: 0.6143 (p90) cc_final: 0.5201 (p90) REVERT: H 181 GLN cc_start: 0.7514 (tt0) cc_final: 0.6821 (mt0) REVERT: I 55 ASN cc_start: 0.8275 (t0) cc_final: 0.8024 (t0) REVERT: I 167 SER cc_start: 0.8199 (t) cc_final: 0.7767 (m) REVERT: J 181 GLN cc_start: 0.7696 (tt0) cc_final: 0.6834 (mt0) REVERT: J 185 LEU cc_start: 0.8345 (mp) cc_final: 0.7805 (mt) REVERT: J 219 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6043 (tppt) REVERT: K 145 TYR cc_start: 0.7064 (t80) cc_final: 0.6558 (t80) REVERT: L 10 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: L 181 GLN cc_start: 0.7699 (tt0) cc_final: 0.6456 (mt0) outliers start: 63 outliers final: 36 residues processed: 307 average time/residue: 0.7228 time to fit residues: 248.8651 Evaluate side-chains 293 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 231 optimal weight: 0.0980 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 245 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN D 125 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN F 125 GLN G 143 ASN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.146285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101763 restraints weight = 30045.919| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.63 r_work: 0.2784 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22092 Z= 0.145 Angle : 0.625 11.197 30108 Z= 0.305 Chirality : 0.047 0.425 3507 Planarity : 0.004 0.040 3777 Dihedral : 4.749 26.362 2903 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.57 % Allowed : 11.21 % Favored : 86.22 % 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: -0.24 (0.16), residues: 2670 helix: 2.36 (0.27), residues: 381 sheet: 0.10 (0.18), residues: 807 loop : -0.99 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 123 TYR 0.020 0.001 TYR A 100 PHE 0.014 0.001 PHE D 9 TRP 0.009 0.001 TRP H 47 HIS 0.014 0.001 HIS I 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (22008) covalent geometry : angle 0.60339 / 0.30 (29886) SS BOND : bond 0.00447 / 0.34 ( 30) SS BOND : angle 1.18582 / 0.71 ( 60) hydrogen bonds : bond 0.03556 / 2.33 ( 872) hydrogen bonds : angle 5.40792 / 3.81 ( 2319) link_ALPHA1-2 : bond 0.00170 / 0.09 ( 3) link_ALPHA1-2 : angle 1.60077 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00204 / 0.11 ( 9) link_ALPHA1-3 : angle 2.61811 / 1.39 ( 27) link_ALPHA1-6 : bond 0.00379 / 0.23 ( 9) link_ALPHA1-6 : angle 1.86757 / 1.09 ( 27) link_BETA1-4 : bond 0.00292 / 0.19 ( 15) link_BETA1-4 : angle 1.55360 / 1.01 ( 45) link_NAG-ASN : bond 0.00656 / 0.38 ( 18) link_NAG-ASN : angle 2.61309 / 1.77 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 0.998 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8441 (m-30) cc_final: 0.8218 (m-30) REVERT: A 104 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7917 (t0) REVERT: A 189 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 280 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8471 (tp30) REVERT: B 17 MET cc_start: 0.8627 (ttm) cc_final: 0.7950 (ttm) REVERT: B 121 LYS cc_start: 0.9158 (ttpt) cc_final: 0.8729 (ttpt) REVERT: C 35 GLU cc_start: 0.8653 (tt0) cc_final: 0.8333 (tt0) REVERT: C 77 ASP cc_start: 0.8253 (m-30) cc_final: 0.7971 (m-30) REVERT: C 173 ASN cc_start: 0.8565 (p0) cc_final: 0.8078 (t0) REVERT: C 307 LYS cc_start: 0.8989 (mttp) cc_final: 0.8612 (mmtt) REVERT: D 17 MET cc_start: 0.8445 (tpp) cc_final: 0.8065 (ttm) REVERT: D 65 GLN cc_start: 0.9199 (mt0) cc_final: 0.8906 (mt0) REVERT: D 150 GLU cc_start: 0.7787 (pp20) cc_final: 0.6851 (tm-30) REVERT: E 31 ASP cc_start: 0.8473 (m-30) cc_final: 0.8116 (m-30) REVERT: E 32 ASP cc_start: 0.8514 (m-30) cc_final: 0.8224 (m-30) REVERT: E 40 THR cc_start: 0.9400 (t) cc_final: 0.9151 (p) REVERT: E 41 GLU cc_start: 0.9075 (tp30) cc_final: 0.8862 (mm-30) REVERT: E 189 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8672 (tp40) REVERT: F 17 MET cc_start: 0.8708 (ttm) cc_final: 0.8389 (ttm) REVERT: F 133 MET cc_start: 0.9287 (mtm) cc_final: 0.8992 (mtp) REVERT: F 150 GLU cc_start: 0.7829 (pp20) cc_final: 0.7013 (tp30) REVERT: H 81 MET cc_start: 0.9198 (ttp) cc_final: 0.8913 (ttt) REVERT: H 155 TYR cc_start: 0.6116 (p90) cc_final: 0.5156 (p90) REVERT: H 181 GLN cc_start: 0.7525 (tt0) cc_final: 0.6856 (mt0) REVERT: I 167 SER cc_start: 0.8222 (t) cc_final: 0.7831 (m) REVERT: J 181 GLN cc_start: 0.7722 (tt0) cc_final: 0.6842 (mt0) REVERT: J 185 LEU cc_start: 0.8362 (mp) cc_final: 0.7817 (mt) REVERT: K 107 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8309 (mtpt) REVERT: K 145 TYR cc_start: 0.7224 (t80) cc_final: 0.6775 (t80) REVERT: L 181 GLN cc_start: 0.7742 (tt0) cc_final: 0.6625 (mt0) outliers start: 60 outliers final: 40 residues processed: 301 average time/residue: 0.6975 time to fit residues: 236.8472 Evaluate side-chains 299 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN G 36 HIS ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 HIS K 36 HIS K 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098540 restraints weight = 30056.541| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.52 r_work: 0.2668 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 22092 Z= 0.316 Angle : 0.733 10.745 30108 Z= 0.357 Chirality : 0.051 0.332 3507 Planarity : 0.005 0.047 3777 Dihedral : 5.055 27.131 2903 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.74 % Allowed : 13.31 % Favored : 83.95 % 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: -0.46 (0.16), residues: 2670 helix: 1.93 (0.26), residues: 381 sheet: -0.02 (0.18), residues: 819 loop : -1.09 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 321 TYR 0.023 0.002 TYR A 100 PHE 0.019 0.002 PHE D 9 TRP 0.015 0.002 TRP B 92 HIS 0.018 0.002 HIS I 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.32 (22008) covalent geometry : angle 0.71001 / 0.35 (29886) SS BOND : bond 0.00677 / 0.51 ( 30) SS BOND : angle 1.60091 / 1.01 ( 60) hydrogen bonds : bond 0.04167 / 2.75 ( 872) hydrogen bonds : angle 5.55915 / 3.91 ( 2319) link_ALPHA1-2 : bond 0.00072 / 0.04 ( 3) link_ALPHA1-2 : angle 1.77932 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00366 / 0.20 ( 9) link_ALPHA1-3 : angle 2.87381 / 1.52 ( 27) link_ALPHA1-6 : bond 0.00429 / 0.29 ( 9) link_ALPHA1-6 : angle 1.87298 / 1.14 ( 27) link_BETA1-4 : bond 0.00383 / 0.24 ( 15) link_BETA1-4 : angle 2.01139 / 1.26 ( 45) link_NAG-ASN : bond 0.00825 / 0.52 ( 18) link_NAG-ASN : angle 2.80891 / 1.85 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 0.712 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: symmetry clash REVERT: A 31 ASP cc_start: 0.8539 (m-30) cc_final: 0.8283 (m-30) REVERT: A 189 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8650 (tm-30) REVERT: B 17 MET cc_start: 0.8724 (ttm) cc_final: 0.7977 (ttm) REVERT: B 110 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8784 (tp) REVERT: B 117 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8477 (mttm) REVERT: B 150 GLU cc_start: 0.7760 (pp20) cc_final: 0.6918 (tp30) REVERT: C 35 GLU cc_start: 0.8725 (tt0) cc_final: 0.8359 (tt0) REVERT: C 77 ASP cc_start: 0.8172 (m-30) cc_final: 0.7863 (m-30) REVERT: C 173 ASN cc_start: 0.8591 (p0) cc_final: 0.7849 (t0) REVERT: C 260 MET cc_start: 0.9297 (mtp) cc_final: 0.9046 (mtp) REVERT: D 12 ASN cc_start: 0.7961 (t0) cc_final: 0.7443 (t0) REVERT: D 17 MET cc_start: 0.8497 (tpp) cc_final: 0.7778 (ttm) REVERT: D 150 GLU cc_start: 0.7758 (pp20) cc_final: 0.6909 (tm-30) REVERT: E 31 ASP cc_start: 0.8400 (m-30) cc_final: 0.7939 (m-30) REVERT: E 32 ASP cc_start: 0.8620 (m-30) cc_final: 0.8297 (m-30) REVERT: E 40 THR cc_start: 0.9310 (t) cc_final: 0.9062 (p) REVERT: E 189 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8266 (tm-30) REVERT: F 12 ASN cc_start: 0.7927 (t0) cc_final: 0.7446 (m110) REVERT: F 17 MET cc_start: 0.8729 (ttm) cc_final: 0.8473 (ttm) REVERT: F 62 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8594 (mttp) REVERT: F 71 SER cc_start: 0.9320 (m) cc_final: 0.9058 (p) REVERT: F 112 ASP cc_start: 0.9081 (t70) cc_final: 0.8808 (t0) REVERT: F 121 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8460 (tttm) REVERT: F 133 MET cc_start: 0.9310 (mtm) cc_final: 0.8961 (mtp) REVERT: F 150 GLU cc_start: 0.7730 (pp20) cc_final: 0.6919 (tp30) REVERT: G 16 GLN cc_start: 0.7030 (pm20) cc_final: 0.6718 (pm20) REVERT: H 81 MET cc_start: 0.9256 (ttp) cc_final: 0.8955 (ttt) REVERT: H 87 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7555 (mtp85) REVERT: H 155 TYR cc_start: 0.5984 (p90) cc_final: 0.5007 (p90) REVERT: I 22 CYS cc_start: 0.7476 (t) cc_final: 0.7049 (t) REVERT: I 84 ASP cc_start: 0.7900 (m-30) cc_final: 0.7690 (m-30) REVERT: I 167 SER cc_start: 0.8145 (t) cc_final: 0.7806 (m) REVERT: J 181 GLN cc_start: 0.7613 (tt0) cc_final: 0.6665 (mt0) REVERT: J 185 LEU cc_start: 0.8256 (mp) cc_final: 0.7655 (mt) REVERT: J 219 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6032 (tppt) REVERT: K 141 LEU cc_start: 0.6259 (mp) cc_final: 0.5609 (tt) REVERT: K 145 TYR cc_start: 0.7255 (t80) cc_final: 0.6696 (t80) REVERT: L 10 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: L 181 GLN cc_start: 0.7636 (tt0) cc_final: 0.6615 (mt0) outliers start: 64 outliers final: 43 residues processed: 298 average time/residue: 0.6807 time to fit residues: 229.1791 Evaluate side-chains 296 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 14 optimal weight: 0.0980 chunk 114 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 164 optimal weight: 0.0980 chunk 212 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN B 125 GLN C 197 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS K 36 HIS K 81 GLN ** 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 = 0.3756 r_free = 0.3756 target = 0.145946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101645 restraints weight = 29754.219| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.54 r_work: 0.2824 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22092 Z= 0.126 Angle : 0.616 9.672 30108 Z= 0.299 Chirality : 0.046 0.328 3507 Planarity : 0.004 0.040 3777 Dihedral : 4.745 27.668 2903 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.61 % Allowed : 14.33 % Favored : 83.06 % 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: -0.24 (0.16), residues: 2670 helix: 2.31 (0.27), residues: 381 sheet: 0.07 (0.18), residues: 843 loop : -0.99 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 321 TYR 0.018 0.001 TYR A 100 PHE 0.015 0.001 PHE D 9 TRP 0.011 0.001 TRP J 50 HIS 0.009 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (22008) covalent geometry : angle 0.59348 / 0.29 (29886) SS BOND : bond 0.00343 / 0.25 ( 30) SS BOND : angle 1.33299 / 0.89 ( 60) hydrogen bonds : bond 0.03424 / 2.24 ( 872) hydrogen bonds : angle 5.22206 / 3.67 ( 2319) link_ALPHA1-2 : bond 0.00164 / 0.08 ( 3) link_ALPHA1-2 : angle 1.52295 / 0.85 ( 9) link_ALPHA1-3 : bond 0.00235 / 0.12 ( 9) link_ALPHA1-3 : angle 2.68395 / 1.43 ( 27) link_ALPHA1-6 : bond 0.00308 / 0.17 ( 9) link_ALPHA1-6 : angle 1.82840 / 1.07 ( 27) link_BETA1-4 : bond 0.00287 / 0.19 ( 15) link_BETA1-4 : angle 1.47794 / 0.96 ( 45) link_NAG-ASN : bond 0.00623 / 0.36 ( 18) link_NAG-ASN : angle 2.66740 / 1.76 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 0.845 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: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8445 (m-30) cc_final: 0.8230 (m-30) REVERT: A 104 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7937 (t0) REVERT: A 189 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8746 (tm-30) REVERT: B 17 MET cc_start: 0.8766 (ttm) cc_final: 0.8315 (ttm) REVERT: B 150 GLU cc_start: 0.7853 (pp20) cc_final: 0.7115 (tp30) REVERT: C 35 GLU cc_start: 0.8654 (tt0) cc_final: 0.8344 (tt0) REVERT: C 77 ASP cc_start: 0.8248 (m-30) cc_final: 0.8001 (m-30) REVERT: C 173 ASN cc_start: 0.8578 (p0) cc_final: 0.8036 (t0) REVERT: D 12 ASN cc_start: 0.7891 (t0) cc_final: 0.7495 (t0) REVERT: D 17 MET cc_start: 0.8356 (tpp) cc_final: 0.8087 (ttm) REVERT: D 65 GLN cc_start: 0.9186 (mt0) cc_final: 0.8961 (mt0) REVERT: D 150 GLU cc_start: 0.7778 (pp20) cc_final: 0.6939 (tm-30) REVERT: E 31 ASP cc_start: 0.8479 (m-30) cc_final: 0.8277 (m-30) REVERT: E 32 ASP cc_start: 0.8630 (m-30) cc_final: 0.8381 (m-30) REVERT: E 40 THR cc_start: 0.9379 (t) cc_final: 0.9177 (p) REVERT: E 41 GLU cc_start: 0.9078 (tp30) cc_final: 0.8867 (mm-30) REVERT: E 173 ASN cc_start: 0.8535 (p0) cc_final: 0.7547 (t0) REVERT: F 12 ASN cc_start: 0.8079 (t0) cc_final: 0.7653 (m110) REVERT: F 17 MET cc_start: 0.8804 (ttm) cc_final: 0.8566 (ttm) REVERT: F 121 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8575 (tttm) REVERT: F 123 ARG cc_start: 0.8888 (ttp-170) cc_final: 0.8686 (ttp80) REVERT: F 133 MET cc_start: 0.9302 (mtm) cc_final: 0.8989 (mtp) REVERT: H 38 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8298 (ptp-170) REVERT: H 81 MET cc_start: 0.9175 (ttp) cc_final: 0.8908 (ttt) REVERT: H 155 TYR cc_start: 0.6187 (p90) cc_final: 0.5354 (p90) REVERT: I 55 ASN cc_start: 0.7411 (t0) cc_final: 0.7175 (t0) REVERT: I 167 SER cc_start: 0.8316 (t) cc_final: 0.7894 (p) REVERT: J 181 GLN cc_start: 0.7682 (tt0) cc_final: 0.6739 (mt0) REVERT: J 185 LEU cc_start: 0.8377 (mp) cc_final: 0.7813 (mt) REVERT: K 107 LYS cc_start: 0.8657 (mtpm) cc_final: 0.8282 (mtpt) REVERT: K 141 LEU cc_start: 0.6481 (mp) cc_final: 0.5853 (tt) REVERT: K 145 TYR cc_start: 0.7214 (t80) cc_final: 0.6677 (t80) REVERT: L 10 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: L 38 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8158 (ptm160) REVERT: L 90 ASP cc_start: 0.8475 (m-30) cc_final: 0.8204 (m-30) REVERT: L 181 GLN cc_start: 0.7802 (tt0) cc_final: 0.6777 (mt0) outliers start: 61 outliers final: 39 residues processed: 298 average time/residue: 0.6816 time to fit residues: 229.8501 Evaluate side-chains 293 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN F 125 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099051 restraints weight = 29849.268| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.24 r_work: 0.2688 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22092 Z= 0.264 Angle : 0.711 22.450 30108 Z= 0.345 Chirality : 0.050 0.436 3507 Planarity : 0.005 0.041 3777 Dihedral : 4.905 27.952 2903 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.21 % Allowed : 14.93 % Favored : 81.86 % 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: -0.34 (0.16), residues: 2670 helix: 2.06 (0.27), residues: 381 sheet: 0.10 (0.18), residues: 819 loop : -1.04 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 63 TYR 0.023 0.002 TYR A 100 PHE 0.018 0.002 PHE B 9 TRP 0.012 0.002 TRP B 92 HIS 0.006 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 (22008) covalent geometry : angle 0.68344 / 0.34 (29886) SS BOND : bond 0.00608 / 0.45 ( 30) SS BOND : angle 2.49392 / 1.60 ( 60) hydrogen bonds : bond 0.03883 / 2.54 ( 872) hydrogen bonds : angle 5.31297 / 3.74 ( 2319) link_ALPHA1-2 : bond 0.00065 / 0.03 ( 3) link_ALPHA1-2 : angle 1.69842 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00285 / 0.15 ( 9) link_ALPHA1-3 : angle 2.76380 / 1.46 ( 27) link_ALPHA1-6 : bond 0.00338 / 0.24 ( 9) link_ALPHA1-6 : angle 1.82365 / 1.10 ( 27) link_BETA1-4 : bond 0.00346 / 0.22 ( 15) link_BETA1-4 : angle 1.81858 / 1.15 ( 45) link_NAG-ASN : bond 0.00749 / 0.46 ( 18) link_NAG-ASN : angle 2.81986 / 1.88 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 253 time to evaluate : 0.771 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: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8452 (m-30) cc_final: 0.8213 (m-30) REVERT: A 104 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7902 (t0) REVERT: A 189 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8653 (tm-30) REVERT: B 17 MET cc_start: 0.8658 (ttm) cc_final: 0.8198 (ttm) REVERT: B 117 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8464 (mttm) REVERT: B 150 GLU cc_start: 0.7741 (pp20) cc_final: 0.6843 (tp30) REVERT: C 35 GLU cc_start: 0.8730 (tt0) cc_final: 0.8347 (tt0) REVERT: C 77 ASP cc_start: 0.8147 (m-30) cc_final: 0.7859 (m-30) REVERT: C 173 ASN cc_start: 0.8577 (p0) cc_final: 0.7843 (t0) REVERT: D 12 ASN cc_start: 0.7955 (t0) cc_final: 0.7429 (t0) REVERT: D 17 MET cc_start: 0.8313 (tpp) cc_final: 0.7916 (ttm) REVERT: D 150 GLU cc_start: 0.7697 (pp20) cc_final: 0.6634 (tp30) REVERT: E 31 ASP cc_start: 0.8425 (m-30) cc_final: 0.7950 (m-30) REVERT: E 32 ASP cc_start: 0.8594 (m-30) cc_final: 0.8285 (m-30) REVERT: E 40 THR cc_start: 0.9299 (t) cc_final: 0.9044 (p) REVERT: E 173 ASN cc_start: 0.8528 (p0) cc_final: 0.7510 (t0) REVERT: F 12 ASN cc_start: 0.8008 (t0) cc_final: 0.7515 (m-40) REVERT: F 17 MET cc_start: 0.8743 (ttm) cc_final: 0.8494 (ttm) REVERT: F 53 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7009 (p0) REVERT: F 62 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8487 (mttp) REVERT: F 71 SER cc_start: 0.9257 (m) cc_final: 0.8972 (p) REVERT: F 112 ASP cc_start: 0.9044 (t70) cc_final: 0.8803 (t0) REVERT: F 121 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8421 (tttm) REVERT: F 133 MET cc_start: 0.9304 (mtm) cc_final: 0.8946 (mtp) REVERT: G 16 GLN cc_start: 0.7055 (pm20) cc_final: 0.6754 (pm20) REVERT: H 38 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8351 (ptp-170) REVERT: H 81 MET cc_start: 0.9250 (ttp) cc_final: 0.8947 (ttt) REVERT: H 155 TYR cc_start: 0.5981 (p90) cc_final: 0.5242 (p90) REVERT: I 22 CYS cc_start: 0.7679 (t) cc_final: 0.7272 (t) REVERT: I 167 SER cc_start: 0.8075 (t) cc_final: 0.7662 (p) REVERT: J 38 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7820 (ptp-170) REVERT: J 90 ASP cc_start: 0.8359 (m-30) cc_final: 0.8112 (m-30) REVERT: J 181 GLN cc_start: 0.7612 (tt0) cc_final: 0.6649 (mt0) REVERT: J 185 LEU cc_start: 0.8253 (mp) cc_final: 0.7615 (mt) REVERT: K 107 LYS cc_start: 0.8544 (mtpm) cc_final: 0.8155 (mtpt) REVERT: K 141 LEU cc_start: 0.6577 (mp) cc_final: 0.5967 (tt) REVERT: K 145 TYR cc_start: 0.7258 (t80) cc_final: 0.6606 (t80) REVERT: L 10 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: L 38 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8196 (ptm160) REVERT: L 90 ASP cc_start: 0.8420 (m-30) cc_final: 0.8153 (m-30) REVERT: L 181 GLN cc_start: 0.7740 (tt0) cc_final: 0.6676 (mt0) outliers start: 75 outliers final: 49 residues processed: 296 average time/residue: 0.6151 time to fit residues: 206.6587 Evaluate side-chains 304 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 44 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 169 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 132 optimal weight: 0.0270 chunk 200 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN F 125 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS G 40 GLN H 39 GLN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 165 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101912 restraints weight = 29547.683| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.44 r_work: 0.2779 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22092 Z= 0.129 Angle : 0.645 21.281 30108 Z= 0.312 Chirality : 0.047 0.405 3507 Planarity : 0.004 0.041 3777 Dihedral : 4.693 28.243 2903 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.70 % Allowed : 15.92 % Favored : 81.39 % 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 (0.16), residues: 2670 helix: 2.68 (0.26), residues: 363 sheet: 0.02 (0.18), residues: 873 loop : -0.90 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 123 TYR 0.019 0.001 TYR F 162 PHE 0.013 0.001 PHE D 9 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (22008) covalent geometry : angle 0.61671 / 0.30 (29886) SS BOND : bond 0.00535 / 0.40 ( 30) SS BOND : angle 2.51809 / 1.57 ( 60) hydrogen bonds : bond 0.03397 / 2.22 ( 872) hydrogen bonds : angle 5.09429 / 3.58 ( 2319) link_ALPHA1-2 : bond 0.00155 / 0.08 ( 3) link_ALPHA1-2 : angle 1.53699 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00168 / 0.09 ( 9) link_ALPHA1-3 : angle 2.63295 / 1.40 ( 27) link_ALPHA1-6 : bond 0.00320 / 0.19 ( 9) link_ALPHA1-6 : angle 1.79152 / 1.05 ( 27) link_BETA1-4 : bond 0.00292 / 0.20 ( 15) link_BETA1-4 : angle 1.45068 / 0.94 ( 45) link_NAG-ASN : bond 0.00613 / 0.35 ( 18) link_NAG-ASN : angle 2.64824 / 1.73 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 0.563 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 31 ASP cc_start: 0.8505 (m-30) cc_final: 0.8285 (m-30) REVERT: A 104 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7895 (t0) REVERT: A 189 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8733 (tm-30) REVERT: B 17 MET cc_start: 0.8694 (ttm) cc_final: 0.8174 (ttm) REVERT: B 117 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8511 (mttm) REVERT: B 150 GLU cc_start: 0.7842 (pp20) cc_final: 0.7052 (tp30) REVERT: C 35 GLU cc_start: 0.8673 (tt0) cc_final: 0.8325 (tt0) REVERT: C 77 ASP cc_start: 0.8228 (m-30) cc_final: 0.7997 (m-30) REVERT: C 173 ASN cc_start: 0.8564 (p0) cc_final: 0.7984 (t0) REVERT: C 260 MET cc_start: 0.9211 (mtp) cc_final: 0.8991 (mtp) REVERT: D 12 ASN cc_start: 0.7956 (t0) cc_final: 0.7544 (t0) REVERT: D 65 GLN cc_start: 0.9176 (mt0) cc_final: 0.8952 (mt0) REVERT: D 150 GLU cc_start: 0.7767 (pp20) cc_final: 0.6751 (tp30) REVERT: E 31 ASP cc_start: 0.8471 (m-30) cc_final: 0.8168 (m-30) REVERT: E 32 ASP cc_start: 0.8620 (m-30) cc_final: 0.8376 (m-30) REVERT: E 40 THR cc_start: 0.9372 (t) cc_final: 0.9153 (p) REVERT: E 173 ASN cc_start: 0.8468 (p0) cc_final: 0.7635 (t0) REVERT: F 12 ASN cc_start: 0.8084 (t0) cc_final: 0.7633 (m-40) REVERT: F 17 MET cc_start: 0.8824 (ttm) cc_final: 0.8593 (ttm) REVERT: F 53 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7054 (p0) REVERT: F 105 GLN cc_start: 0.8981 (tp40) cc_final: 0.8779 (tp-100) REVERT: F 112 ASP cc_start: 0.9017 (t70) cc_final: 0.8801 (t0) REVERT: F 123 ARG cc_start: 0.8902 (ttp-170) cc_final: 0.8672 (ttp80) REVERT: F 133 MET cc_start: 0.9283 (mtm) cc_final: 0.9010 (mtp) REVERT: G 16 GLN cc_start: 0.7104 (pm20) cc_final: 0.6871 (pm20) REVERT: G 91 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8192 (tm-30) REVERT: H 38 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8313 (ptp-170) REVERT: H 81 MET cc_start: 0.9193 (ttp) cc_final: 0.8916 (ttt) REVERT: H 155 TYR cc_start: 0.6112 (p90) cc_final: 0.5445 (p90) REVERT: I 87 ASP cc_start: 0.8090 (t0) cc_final: 0.7846 (t0) REVERT: I 129 GLN cc_start: 0.4646 (tt0) cc_final: 0.4434 (tm-30) REVERT: J 38 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7830 (ptp-170) REVERT: J 90 ASP cc_start: 0.8447 (m-30) cc_final: 0.8223 (m-30) REVERT: J 180 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7199 (mm) REVERT: J 181 GLN cc_start: 0.7580 (tt0) cc_final: 0.6715 (mt0) REVERT: J 185 LEU cc_start: 0.8337 (mp) cc_final: 0.7760 (mt) REVERT: K 107 LYS cc_start: 0.8465 (mtpm) cc_final: 0.8028 (mtpt) REVERT: K 141 LEU cc_start: 0.6575 (mp) cc_final: 0.5853 (tt) REVERT: K 145 TYR cc_start: 0.7241 (t80) cc_final: 0.6679 (t80) REVERT: L 10 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: L 38 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8204 (ptm160) REVERT: L 90 ASP cc_start: 0.8440 (m-30) cc_final: 0.8174 (m-30) REVERT: L 181 GLN cc_start: 0.7669 (tt0) cc_final: 0.6706 (mt0) outliers start: 63 outliers final: 38 residues processed: 309 average time/residue: 0.5957 time to fit residues: 209.4261 Evaluate side-chains 300 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 264 optimal weight: 0.3980 chunk 245 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS I 81 GLN K 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101761 restraints weight = 29836.695| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.51 r_work: 0.2797 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22092 Z= 0.152 Angle : 0.655 19.538 30108 Z= 0.317 Chirality : 0.047 0.445 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.674 28.939 2903 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.61 % Allowed : 16.69 % Favored : 80.70 % 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 (0.16), residues: 2670 helix: 2.62 (0.26), residues: 366 sheet: 0.04 (0.18), residues: 855 loop : -0.91 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 123 TYR 0.023 0.001 TYR A 100 PHE 0.014 0.001 PHE D 9 TRP 0.008 0.001 TRP I 153 HIS 0.003 0.001 HIS L 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (22008) covalent geometry : angle 0.62683 / 0.31 (29886) SS BOND : bond 0.00441 / 0.31 ( 30) SS BOND : angle 2.44532 / 1.54 ( 60) hydrogen bonds : bond 0.03428 / 2.23 ( 872) hydrogen bonds : angle 5.05017 / 3.55 ( 2319) link_ALPHA1-2 : bond 0.00115 / 0.06 ( 3) link_ALPHA1-2 : angle 1.58857 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00161 / 0.09 ( 9) link_ALPHA1-3 : angle 2.59193 / 1.38 ( 27) link_ALPHA1-6 : bond 0.00316 / 0.20 ( 9) link_ALPHA1-6 : angle 1.80289 / 1.06 ( 27) link_BETA1-4 : bond 0.00297 / 0.20 ( 15) link_BETA1-4 : angle 1.48079 / 0.95 ( 45) link_NAG-ASN : bond 0.00660 / 0.39 ( 18) link_NAG-ASN : angle 2.81161 / 1.84 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 0.778 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: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8432 (m-30) cc_final: 0.8185 (m-30) REVERT: A 104 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7797 (t0) REVERT: A 189 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8660 (tm-30) REVERT: B 17 MET cc_start: 0.8691 (ttm) cc_final: 0.8162 (ttm) REVERT: B 117 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8439 (mttm) REVERT: B 150 GLU cc_start: 0.7769 (pp20) cc_final: 0.6889 (tp30) REVERT: C 35 GLU cc_start: 0.8686 (tt0) cc_final: 0.8291 (tt0) REVERT: C 173 ASN cc_start: 0.8556 (p0) cc_final: 0.7962 (t0) REVERT: C 260 MET cc_start: 0.9257 (mtp) cc_final: 0.9052 (mtp) REVERT: D 12 ASN cc_start: 0.7961 (t0) cc_final: 0.7517 (t0) REVERT: D 53 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7725 (m110) REVERT: D 65 GLN cc_start: 0.9212 (mt0) cc_final: 0.8931 (mt0) REVERT: D 150 GLU cc_start: 0.7743 (pp20) cc_final: 0.7105 (tp30) REVERT: E 31 ASP cc_start: 0.8465 (m-30) cc_final: 0.8158 (m-30) REVERT: E 32 ASP cc_start: 0.8611 (m-30) cc_final: 0.8348 (m-30) REVERT: E 40 THR cc_start: 0.9337 (t) cc_final: 0.9109 (p) REVERT: E 173 ASN cc_start: 0.8460 (p0) cc_final: 0.7644 (t0) REVERT: F 12 ASN cc_start: 0.8066 (t0) cc_final: 0.7577 (t0) REVERT: F 17 MET cc_start: 0.8838 (ttm) cc_final: 0.8592 (ttm) REVERT: F 53 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7025 (p0) REVERT: F 123 ARG cc_start: 0.8870 (ttp-170) cc_final: 0.8611 (ttp80) REVERT: F 133 MET cc_start: 0.9298 (mtm) cc_final: 0.9039 (mtp) REVERT: F 150 GLU cc_start: 0.7889 (pp20) cc_final: 0.6963 (tp30) REVERT: G 16 GLN cc_start: 0.7256 (pm20) cc_final: 0.7054 (pm20) REVERT: H 38 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8337 (ptp-170) REVERT: H 81 MET cc_start: 0.9206 (ttp) cc_final: 0.8903 (ttt) REVERT: H 155 TYR cc_start: 0.6085 (p90) cc_final: 0.5495 (p90) REVERT: I 87 ASP cc_start: 0.8093 (t0) cc_final: 0.7868 (t0) REVERT: J 38 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7823 (ptp-170) REVERT: J 90 ASP cc_start: 0.8418 (m-30) cc_final: 0.8134 (m-30) REVERT: J 180 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7089 (mm) REVERT: J 181 GLN cc_start: 0.7559 (tt0) cc_final: 0.6685 (mt0) REVERT: J 185 LEU cc_start: 0.8319 (mp) cc_final: 0.7709 (mt) REVERT: K 107 LYS cc_start: 0.8436 (mtpm) cc_final: 0.8020 (mtpt) REVERT: K 141 LEU cc_start: 0.6497 (mp) cc_final: 0.5834 (tt) REVERT: K 145 TYR cc_start: 0.7216 (t80) cc_final: 0.6690 (t80) REVERT: L 10 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: L 38 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8170 (ptm160) REVERT: L 90 ASP cc_start: 0.8416 (m-30) cc_final: 0.8148 (m-30) REVERT: L 181 GLN cc_start: 0.7664 (tt0) cc_final: 0.6694 (mt0) outliers start: 61 outliers final: 45 residues processed: 302 average time/residue: 0.6058 time to fit residues: 207.8709 Evaluate side-chains 308 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 40 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 176 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN F 125 GLN G 36 HIS G 91 GLN I 81 GLN I 129 GLN K 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101075 restraints weight = 29895.896| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.54 r_work: 0.2807 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22092 Z= 0.176 Angle : 0.662 18.392 30108 Z= 0.320 Chirality : 0.048 0.386 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.716 30.032 2903 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.82 % Allowed : 16.56 % Favored : 80.62 % 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: -0.17 (0.16), residues: 2670 helix: 2.60 (0.26), residues: 366 sheet: 0.05 (0.18), residues: 855 loop : -0.93 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 123 TYR 0.023 0.002 TYR A 100 PHE 0.014 0.002 PHE D 9 TRP 0.009 0.001 TRP I 153 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (22008) covalent geometry : angle 0.63443 / 0.31 (29886) SS BOND : bond 0.00451 / 0.32 ( 30) SS BOND : angle 2.46172 / 1.52 ( 60) hydrogen bonds : bond 0.03506 / 2.29 ( 872) hydrogen bonds : angle 5.06425 / 3.55 ( 2319) link_ALPHA1-2 : bond 0.00105 / 0.05 ( 3) link_ALPHA1-2 : angle 1.59522 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00178 / 0.10 ( 9) link_ALPHA1-3 : angle 2.60926 / 1.39 ( 27) link_ALPHA1-6 : bond 0.00315 / 0.20 ( 9) link_ALPHA1-6 : angle 1.79431 / 1.06 ( 27) link_BETA1-4 : bond 0.00296 / 0.20 ( 15) link_BETA1-4 : angle 1.55057 / 0.99 ( 45) link_NAG-ASN : bond 0.00681 / 0.40 ( 18) link_NAG-ASN : angle 2.65515 / 1.75 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 0.901 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 31 ASP cc_start: 0.8457 (m-30) cc_final: 0.8223 (m-30) REVERT: A 189 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8736 (tm-30) REVERT: B 17 MET cc_start: 0.8693 (ttm) cc_final: 0.7929 (ttm) REVERT: B 53 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7323 (m110) REVERT: B 117 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8505 (mttm) REVERT: B 150 GLU cc_start: 0.7902 (pp20) cc_final: 0.7156 (tp30) REVERT: C 35 GLU cc_start: 0.8651 (tt0) cc_final: 0.8335 (tt0) REVERT: C 173 ASN cc_start: 0.8554 (p0) cc_final: 0.7995 (t0) REVERT: C 260 MET cc_start: 0.9238 (mtp) cc_final: 0.8994 (mtp) REVERT: D 12 ASN cc_start: 0.7972 (t0) cc_final: 0.7570 (t0) REVERT: D 53 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7697 (m110) REVERT: D 65 GLN cc_start: 0.9184 (mt0) cc_final: 0.8962 (mt0) REVERT: D 150 GLU cc_start: 0.7822 (pp20) cc_final: 0.7228 (tp30) REVERT: E 31 ASP cc_start: 0.8472 (m-30) cc_final: 0.8168 (m-30) REVERT: E 32 ASP cc_start: 0.8597 (m-30) cc_final: 0.8364 (m-30) REVERT: E 40 THR cc_start: 0.9378 (t) cc_final: 0.9160 (p) REVERT: E 173 ASN cc_start: 0.8437 (p0) cc_final: 0.7722 (t0) REVERT: F 12 ASN cc_start: 0.8107 (t0) cc_final: 0.7404 (t0) REVERT: F 17 MET cc_start: 0.8867 (ttm) cc_final: 0.8637 (ttm) REVERT: F 53 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7064 (p0) REVERT: F 123 ARG cc_start: 0.8933 (ttp-170) cc_final: 0.8567 (ttp80) REVERT: F 133 MET cc_start: 0.9295 (mtm) cc_final: 0.9037 (mtp) REVERT: F 150 GLU cc_start: 0.7953 (pp20) cc_final: 0.7058 (tp30) REVERT: G 16 GLN cc_start: 0.7256 (pm20) cc_final: 0.7051 (pm20) REVERT: H 38 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8364 (ptp-170) REVERT: H 81 MET cc_start: 0.9203 (ttp) cc_final: 0.8905 (ttt) REVERT: H 155 TYR cc_start: 0.6159 (p90) cc_final: 0.5636 (p90) REVERT: I 87 ASP cc_start: 0.8159 (t0) cc_final: 0.7889 (t0) REVERT: J 38 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7866 (ptp-170) REVERT: J 90 ASP cc_start: 0.8500 (m-30) cc_final: 0.8255 (m-30) REVERT: J 181 GLN cc_start: 0.7565 (tt0) cc_final: 0.6677 (mt0) REVERT: J 185 LEU cc_start: 0.8349 (mp) cc_final: 0.7732 (mt) REVERT: K 107 LYS cc_start: 0.8469 (mtpm) cc_final: 0.8051 (mtpt) REVERT: K 141 LEU cc_start: 0.6617 (mp) cc_final: 0.5938 (tt) REVERT: K 145 TYR cc_start: 0.7209 (t80) cc_final: 0.6711 (t80) REVERT: L 10 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: L 38 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8205 (ptm160) REVERT: L 90 ASP cc_start: 0.8460 (m-30) cc_final: 0.8207 (m-30) REVERT: L 181 GLN cc_start: 0.7692 (tt0) cc_final: 0.6726 (mt0) REVERT: L 220 LYS cc_start: 0.6003 (mmmt) cc_final: 0.5794 (mtpt) outliers start: 66 outliers final: 46 residues processed: 299 average time/residue: 0.6172 time to fit residues: 209.2078 Evaluate side-chains 306 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 205 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 261 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN F 125 GLN I 81 GLN K 39 GLN K 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100534 restraints weight = 29934.677| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.55 r_work: 0.2715 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22092 Z= 0.205 Angle : 0.687 18.383 30108 Z= 0.333 Chirality : 0.048 0.362 3507 Planarity : 0.004 0.051 3777 Dihedral : 4.781 30.866 2903 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.57 % Allowed : 16.82 % Favored : 80.62 % 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: -0.18 (0.16), residues: 2670 helix: 2.52 (0.26), residues: 366 sheet: 0.07 (0.18), residues: 855 loop : -0.94 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 123 TYR 0.024 0.002 TYR A 100 PHE 0.020 0.002 PHE F 9 TRP 0.010 0.001 TRP B 92 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (22008) covalent geometry : angle 0.65878 / 0.32 (29886) SS BOND : bond 0.00428 / 0.30 ( 30) SS BOND : angle 2.74747 / 1.67 ( 60) hydrogen bonds : bond 0.03645 / 2.38 ( 872) hydrogen bonds : angle 5.10894 / 3.58 ( 2319) link_ALPHA1-2 : bond 0.00076 / 0.04 ( 3) link_ALPHA1-2 : angle 1.62246 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00226 / 0.12 ( 9) link_ALPHA1-3 : angle 2.68080 / 1.42 ( 27) link_ALPHA1-6 : bond 0.00288 / 0.19 ( 9) link_ALPHA1-6 : angle 1.79246 / 1.07 ( 27) link_BETA1-4 : bond 0.00296 / 0.19 ( 15) link_BETA1-4 : angle 1.65417 / 1.06 ( 45) link_NAG-ASN : bond 0.00703 / 0.42 ( 18) link_NAG-ASN : angle 2.63236 / 1.74 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 0.553 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 31 ASP cc_start: 0.8424 (m-30) cc_final: 0.8175 (m-30) REVERT: A 189 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8656 (tm-30) REVERT: B 17 MET cc_start: 0.8650 (ttm) cc_final: 0.8097 (ttm) REVERT: B 53 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7284 (m110) REVERT: B 110 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8772 (tp) REVERT: B 117 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8368 (mttm) REVERT: B 150 GLU cc_start: 0.7749 (pp20) cc_final: 0.6931 (tp30) REVERT: C 35 GLU cc_start: 0.8718 (tt0) cc_final: 0.8335 (tt0) REVERT: C 173 ASN cc_start: 0.8542 (p0) cc_final: 0.7882 (t0) REVERT: C 260 MET cc_start: 0.9242 (mtp) cc_final: 0.8994 (mtp) REVERT: D 12 ASN cc_start: 0.7988 (t0) cc_final: 0.7500 (t0) REVERT: D 53 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7657 (m110) REVERT: D 150 GLU cc_start: 0.7729 (pp20) cc_final: 0.7053 (tp30) REVERT: E 31 ASP cc_start: 0.8476 (m-30) cc_final: 0.8105 (m-30) REVERT: E 32 ASP cc_start: 0.8617 (m-30) cc_final: 0.8334 (m-30) REVERT: E 40 THR cc_start: 0.9324 (t) cc_final: 0.9069 (p) REVERT: E 173 ASN cc_start: 0.8398 (p0) cc_final: 0.7633 (t0) REVERT: F 12 ASN cc_start: 0.7954 (t0) cc_final: 0.7241 (t0) REVERT: F 17 MET cc_start: 0.8805 (ttm) cc_final: 0.8561 (ttm) REVERT: F 53 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6982 (p0) REVERT: F 105 GLN cc_start: 0.8819 (tp40) cc_final: 0.8571 (tp40) REVERT: F 123 ARG cc_start: 0.8915 (ttp-170) cc_final: 0.8485 (ttp80) REVERT: F 133 MET cc_start: 0.9297 (mtm) cc_final: 0.9004 (mtp) REVERT: F 150 GLU cc_start: 0.7819 (pp20) cc_final: 0.6891 (tp30) REVERT: G 16 GLN cc_start: 0.7242 (pm20) cc_final: 0.7026 (pm20) REVERT: H 38 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8351 (ptp-170) REVERT: H 55 ASP cc_start: 0.8699 (p0) cc_final: 0.8402 (p0) REVERT: H 81 MET cc_start: 0.9257 (ttp) cc_final: 0.8913 (ttt) REVERT: I 87 ASP cc_start: 0.8147 (t0) cc_final: 0.7846 (t0) REVERT: J 38 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7853 (ptp-170) REVERT: J 90 ASP cc_start: 0.8402 (m-30) cc_final: 0.8127 (m-30) REVERT: J 181 GLN cc_start: 0.7511 (tt0) cc_final: 0.6617 (mt0) REVERT: J 185 LEU cc_start: 0.8269 (mp) cc_final: 0.7612 (mt) REVERT: K 107 LYS cc_start: 0.8506 (mtpm) cc_final: 0.8121 (mtpt) REVERT: K 141 LEU cc_start: 0.6541 (mp) cc_final: 0.5896 (tt) REVERT: K 145 TYR cc_start: 0.7268 (t80) cc_final: 0.6661 (t80) REVERT: L 10 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: L 38 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8190 (ptm160) REVERT: L 83 MET cc_start: 0.8781 (mmt) cc_final: 0.8434 (mmt) REVERT: L 90 ASP cc_start: 0.8387 (m-30) cc_final: 0.8144 (m-30) REVERT: L 181 GLN cc_start: 0.7657 (tt0) cc_final: 0.6665 (mt0) outliers start: 60 outliers final: 47 residues processed: 286 average time/residue: 0.6571 time to fit residues: 212.1578 Evaluate side-chains 301 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 245 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 10 GLU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 160 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 75 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN I 81 GLN K 39 GLN K 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101787 restraints weight = 29908.765| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.51 r_work: 0.2802 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22092 Z= 0.151 Angle : 0.661 17.317 30108 Z= 0.320 Chirality : 0.047 0.356 3507 Planarity : 0.004 0.052 3777 Dihedral : 4.704 31.090 2903 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.65 % Allowed : 16.86 % Favored : 80.49 % 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: -0.12 (0.16), residues: 2670 helix: 2.64 (0.26), residues: 366 sheet: 0.10 (0.18), residues: 855 loop : -0.91 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 123 TYR 0.023 0.001 TYR A 100 PHE 0.014 0.001 PHE D 9 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (22008) covalent geometry : angle 0.63350 / 0.31 (29886) SS BOND : bond 0.00341 / 0.23 ( 30) SS BOND : angle 2.61543 / 1.59 ( 60) hydrogen bonds : bond 0.03423 / 2.23 ( 872) hydrogen bonds : angle 5.00782 / 3.51 ( 2319) link_ALPHA1-2 : bond 0.00121 / 0.06 ( 3) link_ALPHA1-2 : angle 1.57340 / 0.88 ( 9) link_ALPHA1-3 : bond 0.00167 / 0.09 ( 9) link_ALPHA1-3 : angle 2.62785 / 1.40 ( 27) link_ALPHA1-6 : bond 0.00295 / 0.18 ( 9) link_ALPHA1-6 : angle 1.79391 / 1.06 ( 27) link_BETA1-4 : bond 0.00297 / 0.20 ( 15) link_BETA1-4 : angle 1.48504 / 0.96 ( 45) link_NAG-ASN : bond 0.00639 / 0.37 ( 18) link_NAG-ASN : angle 2.56932 / 1.70 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9771.23 seconds wall clock time: 167 minutes 3.10 seconds (10023.10 seconds total)