Starting phenix.real_space_refine on Fri Sep 19 00:50:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k39_22653/09_2025/7k39_22653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k39_22653/09_2025/7k39_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k39_22653/09_2025/7k39_22653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k39_22653/09_2025/7k39_22653.map" model { file = "/net/cci-nas-00/data/ceres_data/7k39_22653/09_2025/7k39_22653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k39_22653/09_2025/7k39_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-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 24 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 24 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 24 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.45, 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: 1.64 Conformation dependent library (CDL) restraints added in 985.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.66 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: 3.92 Time building geometry restraints manager: 2.21 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 - 21.89: 12943 21.89 - 43.79: 722 43.79 - 65.68: 105 65.68 - 87.58: 51 87.58 - 109.47: 24 Dihedral angle restraints: 13845 sinusoidal: 6087 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 13842 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 19.850 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 14.867 109.474 8793 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 aren 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 covalent geometry : bond 0.00747 (22008) covalent geometry : angle 0.78359 (29886) SS BOND : bond 0.03604 ( 30) SS BOND : angle 2.18695 ( 60) hydrogen bonds : bond 0.13969 ( 872) hydrogen bonds : angle 7.01230 ( 2319) link_ALPHA1-2 : bond 0.00214 ( 3) link_ALPHA1-2 : angle 2.04435 ( 9) link_ALPHA1-3 : bond 0.00323 ( 9) link_ALPHA1-3 : angle 3.69514 ( 27) link_ALPHA1-6 : bond 0.00520 ( 9) link_ALPHA1-6 : angle 2.68794 ( 27) link_BETA1-4 : bond 0.00437 ( 15) link_BETA1-4 : angle 1.76184 ( 45) link_NAG-ASN : bond 0.00755 ( 18) link_NAG-ASN : angle 3.09130 ( 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 : 0.664 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: 0.8749 (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: 0.8133 (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: 0.8175 (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: 0.7029 (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: 0.8452 (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: 0.6776 time to fit residues: 310.5380 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 : 0.769 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 12 ASN B 125 GLN C 191 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101352 restraints weight = 30004.201| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.57 r_work: 0.2794 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22092 Z= 0.162 Angle : 0.670 9.188 30108 Z= 0.325 Chirality : 0.048 0.374 3507 Planarity : 0.004 0.038 3777 Dihedral : 10.867 79.939 3983 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.52 % Allowed : 8.60 % Favored : 88.87 % 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 aren not related in a simple way. whole: -0.42 (0.16), residues: 2670 helix: 2.15 (0.26), residues: 381 sheet: -0.05 (0.18), residues: 801 loop : -1.07 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 113 TYR 0.018 0.002 TYR A 100 PHE 0.013 0.001 PHE F 9 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00370 (22008) covalent geometry : angle 0.64243 (29886) SS BOND : bond 0.00442 ( 30) SS BOND : angle 1.46022 ( 60) hydrogen bonds : bond 0.03987 ( 872) hydrogen bonds : angle 5.77998 ( 2319) link_ALPHA1-2 : bond 0.00107 ( 3) link_ALPHA1-2 : angle 1.93958 ( 9) link_ALPHA1-3 : bond 0.00342 ( 9) link_ALPHA1-3 : angle 3.19653 ( 27) link_ALPHA1-6 : bond 0.00402 ( 9) link_ALPHA1-6 : angle 2.40754 ( 27) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 2.00964 ( 45) link_NAG-ASN : bond 0.00728 ( 18) link_NAG-ASN : angle 2.72785 ( 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 338 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 0.846 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: 0.8436 (m-30) cc_final: 0.8222 (m-30) REVERT: A 189 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8677 (tm-30) REVERT: A 280 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8552 (tp30) REVERT: B 121 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8709 (ttpt) REVERT: C 35 GLU cc_start: 0.8642 (tt0) cc_final: 0.8284 (tt0) REVERT: C 77 ASP cc_start: 0.8251 (m-30) cc_final: 0.7972 (m-30) REVERT: C 173 ASN cc_start: 0.8602 (p0) cc_final: 0.8050 (t0) REVERT: C 307 LYS cc_start: 0.8945 (mttp) cc_final: 0.8523 (mmtt) REVERT: D 17 MET cc_start: 0.8607 (tpp) cc_final: 0.7912 (ttm) REVERT: D 47 GLN cc_start: 0.9168 (mt0) cc_final: 0.8807 (mt0) REVERT: D 65 GLN cc_start: 0.9223 (mt0) cc_final: 0.8930 (mt0) REVERT: D 150 GLU cc_start: 0.7790 (pp20) cc_final: 0.6805 (tm-30) REVERT: E 31 ASP cc_start: 0.8438 (m-30) cc_final: 0.8096 (m-30) REVERT: E 40 THR cc_start: 0.9368 (t) cc_final: 0.9133 (p) REVERT: E 189 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8690 (tp40) REVERT: F 17 MET cc_start: 0.8763 (ttm) cc_final: 0.8421 (ttm) REVERT: F 47 GLN cc_start: 0.9014 (mt0) cc_final: 0.8616 (mt0) REVERT: F 115 MET cc_start: 0.9160 (tpt) cc_final: 0.8920 (tpt) REVERT: F 133 MET cc_start: 0.9263 (mtm) cc_final: 0.9035 (mtp) REVERT: F 150 GLU cc_start: 0.7859 (pp20) cc_final: 0.7128 (tp30) REVERT: G 16 GLN cc_start: 0.7163 (pm20) cc_final: 0.6798 (pm20) REVERT: G 81 GLN cc_start: 0.7463 (pm20) cc_final: 0.6865 (pm20) REVERT: H 81 MET cc_start: 0.9210 (ttp) cc_final: 0.8907 (ttt) REVERT: H 181 GLN cc_start: 0.7511 (tt0) cc_final: 0.6826 (mt0) REVERT: I 55 ASN cc_start: 0.8284 (t0) cc_final: 0.8030 (t0) REVERT: I 167 SER cc_start: 0.8202 (t) cc_final: 0.7770 (m) REVERT: J 181 GLN cc_start: 0.7700 (tt0) cc_final: 0.6820 (mt0) REVERT: J 185 LEU cc_start: 0.8365 (mp) cc_final: 0.7826 (mt) REVERT: J 219 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6053 (tppt) REVERT: K 145 TYR cc_start: 0.7059 (t80) cc_final: 0.6562 (t80) REVERT: L 10 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: L 62 LYS cc_start: 0.8795 (tppt) cc_final: 0.8552 (tttp) REVERT: L 181 GLN cc_start: 0.7704 (tt0) cc_final: 0.6461 (mt0) outliers start: 59 outliers final: 35 residues processed: 306 average time/residue: 0.6668 time to fit residues: 227.8535 Evaluate side-chains 288 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 321 ARG 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 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 180 LEU 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: 0.0020 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** 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 143 ASN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS 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 = 0.3756 r_free = 0.3756 target = 0.145841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101433 restraints weight = 30074.974| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.58 r_work: 0.2788 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22092 Z= 0.159 Angle : 0.645 11.207 30108 Z= 0.313 Chirality : 0.048 0.429 3507 Planarity : 0.004 0.040 3777 Dihedral : 10.146 72.943 3983 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.65 % Allowed : 11.30 % Favored : 86.05 % 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 aren not related in a simple way. whole: -0.27 (0.16), residues: 2670 helix: 2.30 (0.27), residues: 381 sheet: 0.08 (0.18), residues: 807 loop : -1.01 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 38 TYR 0.019 0.001 TYR A 100 PHE 0.015 0.002 PHE D 9 TRP 0.009 0.001 TRP H 47 HIS 0.016 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00366 (22008) covalent geometry : angle 0.62018 (29886) SS BOND : bond 0.00603 ( 30) SS BOND : angle 1.16305 ( 60) hydrogen bonds : bond 0.03626 ( 872) hydrogen bonds : angle 5.46423 ( 2319) link_ALPHA1-2 : bond 0.00109 ( 3) link_ALPHA1-2 : angle 1.75222 ( 9) link_ALPHA1-3 : bond 0.00435 ( 9) link_ALPHA1-3 : angle 2.93738 ( 27) link_ALPHA1-6 : bond 0.00505 ( 9) link_ALPHA1-6 : angle 2.23281 ( 27) link_BETA1-4 : bond 0.00334 ( 15) link_BETA1-4 : angle 1.84141 ( 45) link_NAG-ASN : bond 0.00637 ( 18) link_NAG-ASN : angle 2.69149 ( 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 328 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 0.659 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: A 31 ASP cc_start: 0.8437 (m-30) cc_final: 0.8189 (m-30) REVERT: A 104 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7933 (t0) REVERT: A 189 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8663 (tm-30) REVERT: A 280 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8476 (tp30) REVERT: B 17 MET cc_start: 0.8618 (ttm) cc_final: 0.7941 (ttm) REVERT: C 35 GLU cc_start: 0.8651 (tt0) cc_final: 0.8337 (tt0) REVERT: C 77 ASP cc_start: 0.8233 (m-30) cc_final: 0.7944 (m-30) REVERT: C 173 ASN cc_start: 0.8562 (p0) cc_final: 0.8006 (t0) REVERT: C 307 LYS cc_start: 0.8991 (mttp) cc_final: 0.8618 (mmtt) REVERT: D 17 MET cc_start: 0.8477 (tpp) cc_final: 0.8075 (ttm) REVERT: D 47 GLN cc_start: 0.9194 (mt0) cc_final: 0.8816 (mt0) REVERT: D 65 GLN cc_start: 0.9201 (mt0) cc_final: 0.8907 (mt0) REVERT: D 150 GLU cc_start: 0.7797 (pp20) cc_final: 0.6863 (tm-30) REVERT: E 31 ASP cc_start: 0.8476 (m-30) cc_final: 0.8106 (m-30) REVERT: E 32 ASP cc_start: 0.8495 (m-30) cc_final: 0.8212 (m-30) REVERT: E 40 THR cc_start: 0.9400 (t) cc_final: 0.9156 (p) REVERT: E 189 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8675 (tp40) REVERT: F 17 MET cc_start: 0.8707 (ttm) cc_final: 0.8398 (ttm) REVERT: F 47 GLN cc_start: 0.8907 (mt0) cc_final: 0.8677 (mt0) REVERT: F 133 MET cc_start: 0.9279 (mtm) cc_final: 0.8996 (mtp) REVERT: F 150 GLU cc_start: 0.7846 (pp20) cc_final: 0.7060 (tp30) REVERT: G 16 GLN cc_start: 0.7174 (pm20) cc_final: 0.6914 (pm20) REVERT: H 38 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8314 (ptp-170) REVERT: H 81 MET cc_start: 0.9202 (ttp) cc_final: 0.8912 (ttt) REVERT: H 155 TYR cc_start: 0.6111 (p90) cc_final: 0.5156 (p90) REVERT: H 181 GLN cc_start: 0.7522 (tt0) cc_final: 0.6850 (mt0) REVERT: I 167 SER cc_start: 0.8260 (t) cc_final: 0.7854 (m) REVERT: J 181 GLN cc_start: 0.7708 (tt0) cc_final: 0.6830 (mt0) REVERT: J 185 LEU cc_start: 0.8338 (mp) cc_final: 0.7779 (mt) REVERT: K 107 LYS cc_start: 0.8687 (mtpm) cc_final: 0.8269 (mtpt) REVERT: K 145 TYR cc_start: 0.7258 (t80) cc_final: 0.6768 (t80) REVERT: L 62 LYS cc_start: 0.8767 (tppt) cc_final: 0.8530 (tttp) REVERT: L 83 MET cc_start: 0.8645 (tpp) cc_final: 0.8090 (mmt) REVERT: L 181 GLN cc_start: 0.7748 (tt0) cc_final: 0.6549 (mt0) outliers start: 62 outliers final: 43 residues processed: 299 average time/residue: 0.6450 time to fit residues: 216.3604 Evaluate side-chains 303 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain E residue 321 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 38 ARG 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 K residue 36 HIS Chi-restraints excluded: chain L residue 38 ARG 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: 0.6980 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 105 GLN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100291 restraints weight = 30022.634| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.60 r_work: 0.2751 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22092 Z= 0.207 Angle : 0.659 9.522 30108 Z= 0.320 Chirality : 0.049 0.324 3507 Planarity : 0.004 0.040 3777 Dihedral : 9.741 68.785 3983 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.82 % Allowed : 12.71 % Favored : 84.47 % 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 aren not related in a simple way. whole: -0.30 (0.16), residues: 2670 helix: 2.23 (0.27), residues: 381 sheet: 0.04 (0.18), residues: 819 loop : -1.00 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 123 TYR 0.021 0.002 TYR A 100 PHE 0.016 0.002 PHE D 9 TRP 0.010 0.002 TRP B 92 HIS 0.017 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00486 (22008) covalent geometry : angle 0.63416 (29886) SS BOND : bond 0.00486 ( 30) SS BOND : angle 1.36246 ( 60) hydrogen bonds : bond 0.03708 ( 872) hydrogen bonds : angle 5.36643 ( 2319) link_ALPHA1-2 : bond 0.00068 ( 3) link_ALPHA1-2 : angle 1.76442 ( 9) link_ALPHA1-3 : bond 0.00469 ( 9) link_ALPHA1-3 : angle 2.96671 ( 27) link_ALPHA1-6 : bond 0.00531 ( 9) link_ALPHA1-6 : angle 2.23154 ( 27) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 1.85723 ( 45) link_NAG-ASN : bond 0.00707 ( 18) link_NAG-ASN : angle 2.70095 ( 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 327 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 261 time to evaluate : 0.790 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: 0.8426 (m-30) cc_final: 0.8167 (m-30) REVERT: A 104 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7899 (t0) REVERT: A 189 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8678 (tm-30) REVERT: B 17 MET cc_start: 0.8593 (ttm) cc_final: 0.7854 (ttm) REVERT: C 35 GLU cc_start: 0.8716 (tt0) cc_final: 0.8382 (tt0) REVERT: C 77 ASP cc_start: 0.8304 (m-30) cc_final: 0.8025 (m-30) REVERT: C 173 ASN cc_start: 0.8577 (p0) cc_final: 0.7965 (t0) REVERT: C 260 MET cc_start: 0.9237 (mtp) cc_final: 0.8997 (mtp) REVERT: D 17 MET cc_start: 0.8385 (tpp) cc_final: 0.8008 (ttm) REVERT: D 47 GLN cc_start: 0.9221 (mt0) cc_final: 0.8848 (mt0) REVERT: D 65 GLN cc_start: 0.9240 (mt0) cc_final: 0.8897 (mt0) REVERT: D 150 GLU cc_start: 0.7750 (pp20) cc_final: 0.6895 (tm-30) REVERT: E 31 ASP cc_start: 0.8482 (m-30) cc_final: 0.8098 (m-30) REVERT: E 32 ASP cc_start: 0.8635 (m-30) cc_final: 0.8353 (m-30) REVERT: E 40 THR cc_start: 0.9346 (t) cc_final: 0.9111 (p) REVERT: E 189 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8410 (tm-30) REVERT: F 12 ASN cc_start: 0.7961 (t0) cc_final: 0.7518 (m110) REVERT: F 17 MET cc_start: 0.8758 (ttm) cc_final: 0.8495 (ttm) REVERT: F 62 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8469 (mttp) REVERT: F 133 MET cc_start: 0.9291 (mtm) cc_final: 0.8988 (mtp) REVERT: F 150 GLU cc_start: 0.7806 (pp20) cc_final: 0.7070 (tp30) REVERT: H 38 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8319 (ptp-170) REVERT: H 81 MET cc_start: 0.9216 (ttp) cc_final: 0.8923 (ttt) REVERT: H 155 TYR cc_start: 0.6035 (p90) cc_final: 0.5110 (p90) REVERT: H 181 GLN cc_start: 0.7553 (tt0) cc_final: 0.6820 (mt0) REVERT: I 22 CYS cc_start: 0.7325 (t) cc_final: 0.6924 (t) REVERT: I 167 SER cc_start: 0.8187 (t) cc_final: 0.7836 (m) REVERT: J 155 TYR cc_start: 0.6154 (p90) cc_final: 0.5941 (p90) REVERT: J 181 GLN cc_start: 0.7698 (tt0) cc_final: 0.6801 (mt0) REVERT: J 185 LEU cc_start: 0.8315 (mp) cc_final: 0.7735 (mt) REVERT: K 107 LYS cc_start: 0.8604 (mtpm) cc_final: 0.8207 (mtpt) REVERT: K 141 LEU cc_start: 0.6229 (mp) cc_final: 0.5584 (tt) REVERT: K 145 TYR cc_start: 0.7230 (t80) cc_final: 0.6529 (t80) REVERT: L 10 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: L 83 MET cc_start: 0.8592 (tpp) cc_final: 0.8115 (mmt) REVERT: L 181 GLN cc_start: 0.7729 (tt0) cc_final: 0.6611 (mt0) REVERT: L 203 THR cc_start: 0.4803 (OUTLIER) cc_final: 0.4332 (m) outliers start: 66 outliers final: 43 residues processed: 298 average time/residue: 0.6145 time to fit residues: 206.2160 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 : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 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 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 18 ILE 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 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 42 GLN 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 38 ARG Chi-restraints excluded: chain H residue 62 LYS 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 J residue 24 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL 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 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 Chi-restraints excluded: chain L residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 14 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 197 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102373 restraints weight = 29777.566| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.47 r_work: 0.2838 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2045 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= 0.145 Angle : 0.622 9.787 30108 Z= 0.300 Chirality : 0.047 0.376 3507 Planarity : 0.004 0.041 3777 Dihedral : 8.997 60.731 3983 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.61 % Allowed : 14.29 % Favored : 83.10 % 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 aren not related in a simple way. whole: -0.15 (0.16), residues: 2670 helix: 2.81 (0.26), residues: 363 sheet: 0.11 (0.18), residues: 825 loop : -0.99 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 321 TYR 0.021 0.001 TYR A 100 PHE 0.014 0.001 PHE D 9 TRP 0.009 0.001 TRP J 50 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00334 (22008) covalent geometry : angle 0.59725 (29886) SS BOND : bond 0.00381 ( 30) SS BOND : angle 1.43043 ( 60) hydrogen bonds : bond 0.03398 ( 872) hydrogen bonds : angle 5.12938 ( 2319) link_ALPHA1-2 : bond 0.00139 ( 3) link_ALPHA1-2 : angle 1.68559 ( 9) link_ALPHA1-3 : bond 0.00563 ( 9) link_ALPHA1-3 : angle 2.88044 ( 27) link_ALPHA1-6 : bond 0.00579 ( 9) link_ALPHA1-6 : angle 2.19232 ( 27) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.61920 ( 45) link_NAG-ASN : bond 0.00740 ( 18) link_NAG-ASN : angle 2.66766 ( 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 : 0.502 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: 0.8437 (m-30) cc_final: 0.8203 (m-30) REVERT: A 104 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7951 (t0) REVERT: A 189 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8700 (tm-30) REVERT: B 17 MET cc_start: 0.8817 (ttm) cc_final: 0.8273 (ttm) REVERT: B 150 GLU cc_start: 0.7876 (pp20) cc_final: 0.7142 (tp30) REVERT: C 35 GLU cc_start: 0.8630 (tt0) cc_final: 0.8333 (tt0) REVERT: C 77 ASP cc_start: 0.8296 (m-30) cc_final: 0.8049 (m-30) REVERT: C 173 ASN cc_start: 0.8554 (p0) cc_final: 0.8080 (t0) REVERT: D 12 ASN cc_start: 0.7866 (t0) cc_final: 0.7496 (t0) REVERT: D 65 GLN cc_start: 0.9183 (mt0) cc_final: 0.8915 (mt0) REVERT: D 150 GLU cc_start: 0.7822 (pp20) cc_final: 0.7014 (tm-30) REVERT: E 32 ASP cc_start: 0.8624 (m-30) cc_final: 0.8396 (m-30) REVERT: E 40 THR cc_start: 0.9386 (t) cc_final: 0.9179 (p) REVERT: E 173 ASN cc_start: 0.8556 (p0) cc_final: 0.7544 (t0) REVERT: F 12 ASN cc_start: 0.7963 (t0) cc_final: 0.7574 (m-40) REVERT: F 17 MET cc_start: 0.8839 (ttm) cc_final: 0.8605 (ttm) REVERT: F 133 MET cc_start: 0.9257 (mtm) cc_final: 0.8958 (mtp) REVERT: G 16 GLN cc_start: 0.7148 (pm20) cc_final: 0.6913 (pm20) REVERT: H 38 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8220 (ptp-170) REVERT: H 81 MET cc_start: 0.9164 (ttp) cc_final: 0.8886 (ttt) REVERT: H 114 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8646 (p0) REVERT: H 155 TYR cc_start: 0.6133 (p90) cc_final: 0.5307 (p90) REVERT: I 55 ASN cc_start: 0.7466 (t0) cc_final: 0.7251 (t0) REVERT: I 68 LYS cc_start: 0.8240 (tttm) cc_final: 0.6158 (tptt) REVERT: I 167 SER cc_start: 0.8306 (t) cc_final: 0.7906 (p) REVERT: J 180 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7182 (mm) REVERT: J 181 GLN cc_start: 0.7663 (tt0) cc_final: 0.6753 (mt0) REVERT: J 185 LEU cc_start: 0.8394 (mp) cc_final: 0.7819 (mt) REVERT: K 107 LYS cc_start: 0.8463 (mtpm) cc_final: 0.8088 (mtpt) REVERT: K 141 LEU cc_start: 0.6517 (mp) cc_final: 0.5841 (tt) REVERT: K 145 TYR cc_start: 0.7174 (t80) cc_final: 0.6662 (t80) REVERT: L 10 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: L 83 MET cc_start: 0.8450 (tpp) cc_final: 0.8097 (mmt) REVERT: L 181 GLN cc_start: 0.7800 (tt0) cc_final: 0.6694 (mt0) outliers start: 61 outliers final: 41 residues processed: 295 average time/residue: 0.6222 time to fit residues: 207.1215 Evaluate side-chains 295 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 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 C residue 24 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 18 ILE 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 262 THR 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 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 54 TYR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 114 ASP 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 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 180 LEU 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 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: 0.0060 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 92 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS K 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102682 restraints weight = 29768.357| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.51 r_work: 0.2829 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2174 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= 0.123 Angle : 0.635 20.949 30108 Z= 0.306 Chirality : 0.047 0.426 3507 Planarity : 0.004 0.041 3777 Dihedral : 8.576 56.050 3983 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.52 % Allowed : 15.28 % Favored : 82.20 % 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 aren not related in a simple way. whole: -0.06 (0.16), residues: 2670 helix: 2.84 (0.26), residues: 363 sheet: 0.18 (0.18), residues: 843 loop : -0.93 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 321 TYR 0.021 0.001 TYR A 100 PHE 0.014 0.001 PHE B 3 TRP 0.010 0.001 TRP K 37 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00279 (22008) covalent geometry : angle 0.60575 (29886) SS BOND : bond 0.00476 ( 30) SS BOND : angle 2.37018 ( 60) hydrogen bonds : bond 0.03288 ( 872) hydrogen bonds : angle 5.01365 ( 2319) link_ALPHA1-2 : bond 0.00152 ( 3) link_ALPHA1-2 : angle 1.68173 ( 9) link_ALPHA1-3 : bond 0.00609 ( 9) link_ALPHA1-3 : angle 2.86461 ( 27) link_ALPHA1-6 : bond 0.00598 ( 9) link_ALPHA1-6 : angle 2.13557 ( 27) link_BETA1-4 : bond 0.00325 ( 15) link_BETA1-4 : angle 1.51644 ( 45) link_NAG-ASN : bond 0.00699 ( 18) link_NAG-ASN : angle 2.60995 ( 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: 59 poor density : 269 time to evaluate : 0.833 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: A 31 ASP cc_start: 0.8481 (m-30) cc_final: 0.8230 (m-30) REVERT: A 104 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7920 (t0) REVERT: A 189 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8673 (tm-30) REVERT: B 17 MET cc_start: 0.8819 (ttm) cc_final: 0.8093 (ttm) REVERT: B 150 GLU cc_start: 0.7801 (pp20) cc_final: 0.6975 (tp30) REVERT: C 35 GLU cc_start: 0.8638 (tt0) cc_final: 0.8309 (tt0) REVERT: C 77 ASP cc_start: 0.8277 (m-30) cc_final: 0.8033 (m-30) REVERT: C 126 THR cc_start: 0.8901 (m) cc_final: 0.8674 (p) REVERT: C 173 ASN cc_start: 0.8529 (p0) cc_final: 0.8044 (t0) REVERT: D 65 GLN cc_start: 0.9178 (mt0) cc_final: 0.8919 (mt0) REVERT: D 150 GLU cc_start: 0.7761 (pp20) cc_final: 0.6792 (tp30) REVERT: E 32 ASP cc_start: 0.8581 (m-30) cc_final: 0.8369 (m-30) REVERT: E 40 THR cc_start: 0.9383 (t) cc_final: 0.9165 (p) REVERT: E 173 ASN cc_start: 0.8488 (p0) cc_final: 0.7569 (t0) REVERT: F 12 ASN cc_start: 0.7997 (t0) cc_final: 0.7581 (m-40) REVERT: F 17 MET cc_start: 0.8825 (ttm) cc_final: 0.8589 (ttm) REVERT: F 133 MET cc_start: 0.9246 (mtm) cc_final: 0.8942 (mtp) REVERT: G 16 GLN cc_start: 0.7259 (pm20) cc_final: 0.7032 (pm20) REVERT: G 68 LYS cc_start: 0.8221 (tttt) cc_final: 0.6358 (tptt) REVERT: H 38 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8568 (ptp-170) REVERT: H 81 MET cc_start: 0.9155 (ttp) cc_final: 0.8888 (ttt) REVERT: H 155 TYR cc_start: 0.6098 (p90) cc_final: 0.5440 (p90) REVERT: H 171 SER cc_start: 0.7458 (t) cc_final: 0.7162 (p) REVERT: I 55 ASN cc_start: 0.7340 (t0) cc_final: 0.7129 (t0) REVERT: I 91 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8429 (tm-30) REVERT: I 167 SER cc_start: 0.8244 (t) cc_final: 0.7842 (p) REVERT: J 180 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7294 (mm) REVERT: J 181 GLN cc_start: 0.7682 (tt0) cc_final: 0.6755 (mt0) REVERT: J 185 LEU cc_start: 0.8389 (mp) cc_final: 0.7818 (mt) REVERT: K 107 LYS cc_start: 0.8414 (mtpm) cc_final: 0.8023 (mtpt) REVERT: K 141 LEU cc_start: 0.6554 (mp) cc_final: 0.5892 (tt) REVERT: K 145 TYR cc_start: 0.7349 (t80) cc_final: 0.6803 (t80) REVERT: L 10 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: L 83 MET cc_start: 0.8394 (tpp) cc_final: 0.8085 (mmt) REVERT: L 181 GLN cc_start: 0.7676 (tt0) cc_final: 0.6693 (mt0) outliers start: 59 outliers final: 41 residues processed: 301 average time/residue: 0.6473 time to fit residues: 219.4480 Evaluate side-chains 300 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 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 18 ILE 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 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 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 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 I residue 36 HIS 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 180 LEU Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 10 GLU 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: 0.8980 chunk 178 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS K 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101907 restraints weight = 29574.213| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.49 r_work: 0.2793 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22092 Z= 0.171 Angle : 0.664 21.434 30108 Z= 0.321 Chirality : 0.048 0.402 3507 Planarity : 0.004 0.043 3777 Dihedral : 8.469 56.712 3983 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.57 % Allowed : 15.88 % Favored : 81.56 % 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 aren not related in a simple way. whole: -0.09 (0.16), residues: 2670 helix: 2.82 (0.26), residues: 363 sheet: 0.14 (0.18), residues: 837 loop : -0.93 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 123 TYR 0.023 0.001 TYR A 100 PHE 0.014 0.002 PHE F 9 TRP 0.009 0.001 TRP J 50 HIS 0.006 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00399 (22008) covalent geometry : angle 0.63374 (29886) SS BOND : bond 0.00515 ( 30) SS BOND : angle 2.64128 ( 60) hydrogen bonds : bond 0.03441 ( 872) hydrogen bonds : angle 5.03009 ( 2319) link_ALPHA1-2 : bond 0.00108 ( 3) link_ALPHA1-2 : angle 1.71020 ( 9) link_ALPHA1-3 : bond 0.00581 ( 9) link_ALPHA1-3 : angle 2.87717 ( 27) link_ALPHA1-6 : bond 0.00566 ( 9) link_ALPHA1-6 : angle 2.09172 ( 27) link_BETA1-4 : bond 0.00322 ( 15) link_BETA1-4 : angle 1.59514 ( 45) link_NAG-ASN : bond 0.00671 ( 18) link_NAG-ASN : angle 2.61040 ( 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 323 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8438 (m-30) cc_final: 0.8214 (m-30) REVERT: A 189 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8687 (tm-30) REVERT: B 17 MET cc_start: 0.8827 (ttm) cc_final: 0.8084 (ttm) REVERT: B 150 GLU cc_start: 0.7859 (pp20) cc_final: 0.7003 (tp30) REVERT: C 35 GLU cc_start: 0.8697 (tt0) cc_final: 0.8385 (tt0) REVERT: C 77 ASP cc_start: 0.8267 (m-30) cc_final: 0.8027 (m-30) REVERT: C 126 THR cc_start: 0.8933 (m) cc_final: 0.8693 (p) REVERT: C 173 ASN cc_start: 0.8563 (p0) cc_final: 0.8042 (t0) REVERT: C 260 MET cc_start: 0.9237 (mtp) cc_final: 0.9014 (mtp) REVERT: D 12 ASN cc_start: 0.7868 (t0) cc_final: 0.7433 (t0) REVERT: D 65 GLN cc_start: 0.9185 (mt0) cc_final: 0.8918 (mt0) REVERT: D 150 GLU cc_start: 0.7804 (pp20) cc_final: 0.6867 (tp30) REVERT: E 40 THR cc_start: 0.9382 (t) cc_final: 0.9173 (p) REVERT: E 173 ASN cc_start: 0.8496 (p0) cc_final: 0.7639 (t0) REVERT: F 12 ASN cc_start: 0.8034 (t0) cc_final: 0.7609 (m-40) REVERT: F 17 MET cc_start: 0.8859 (ttm) cc_final: 0.8629 (ttm) REVERT: F 62 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8422 (mttp) REVERT: F 123 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8609 (ttp80) REVERT: F 133 MET cc_start: 0.9269 (mtm) cc_final: 0.8968 (mtp) REVERT: F 150 GLU cc_start: 0.7968 (pp20) cc_final: 0.7078 (tp30) REVERT: G 16 GLN cc_start: 0.7242 (pm20) cc_final: 0.7034 (pm20) REVERT: H 81 MET cc_start: 0.9194 (ttp) cc_final: 0.8907 (ttt) REVERT: H 155 TYR cc_start: 0.6055 (p90) cc_final: 0.5440 (p90) REVERT: I 167 SER cc_start: 0.8182 (t) cc_final: 0.7806 (p) REVERT: J 180 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7151 (mm) REVERT: J 181 GLN cc_start: 0.7684 (tt0) cc_final: 0.6751 (mt0) REVERT: J 185 LEU cc_start: 0.8329 (mp) cc_final: 0.7742 (mt) REVERT: K 107 LYS cc_start: 0.8389 (mtpm) cc_final: 0.8019 (mtpt) REVERT: K 141 LEU cc_start: 0.6516 (mp) cc_final: 0.5810 (tt) REVERT: K 145 TYR cc_start: 0.7305 (t80) cc_final: 0.6832 (t80) REVERT: L 10 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: L 83 MET cc_start: 0.8365 (tpp) cc_final: 0.8027 (mmt) REVERT: L 181 GLN cc_start: 0.7684 (tt0) cc_final: 0.6716 (mt0) outliers start: 60 outliers final: 43 residues processed: 296 average time/residue: 0.6608 time to fit residues: 220.5281 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 : 0.693 ------------------------------------------------------------------------------- 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 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 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 277 CYS 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 208 ARG Chi-restraints excluded: chain E residue 262 THR 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 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 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 I residue 36 HIS 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 180 LEU Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN I 81 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 = 0.3757 r_free = 0.3757 target = 0.145947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101671 restraints weight = 29868.059| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.51 r_work: 0.2812 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22092 Z= 0.166 Angle : 0.659 19.475 30108 Z= 0.319 Chirality : 0.048 0.362 3507 Planarity : 0.004 0.043 3777 Dihedral : 8.295 56.676 3983 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.35 % Allowed : 16.39 % Favored : 81.26 % 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 aren not related in a simple way. whole: -0.06 (0.16), residues: 2670 helix: 2.80 (0.26), residues: 363 sheet: 0.19 (0.18), residues: 837 loop : -0.92 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 123 TYR 0.023 0.001 TYR A 100 PHE 0.014 0.001 PHE D 9 TRP 0.015 0.001 TRP I 37 HIS 0.012 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00386 (22008) covalent geometry : angle 0.62961 (29886) SS BOND : bond 0.00441 ( 30) SS BOND : angle 2.60517 ( 60) hydrogen bonds : bond 0.03446 ( 872) hydrogen bonds : angle 5.01701 ( 2319) link_ALPHA1-2 : bond 0.00115 ( 3) link_ALPHA1-2 : angle 1.70400 ( 9) link_ALPHA1-3 : bond 0.00586 ( 9) link_ALPHA1-3 : angle 2.87879 ( 27) link_ALPHA1-6 : bond 0.00554 ( 9) link_ALPHA1-6 : angle 2.03862 ( 27) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 1.57021 ( 45) link_NAG-ASN : bond 0.00657 ( 18) link_NAG-ASN : angle 2.60688 ( 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 313 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.841 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: 0.8446 (m-30) cc_final: 0.8236 (m-30) REVERT: A 189 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8715 (tm-30) REVERT: B 17 MET cc_start: 0.8719 (ttm) cc_final: 0.8017 (ttm) REVERT: B 117 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8544 (mttm) REVERT: B 150 GLU cc_start: 0.7876 (pp20) cc_final: 0.7113 (tp30) REVERT: C 35 GLU cc_start: 0.8688 (tt0) cc_final: 0.8379 (tt0) REVERT: C 77 ASP cc_start: 0.8243 (m-30) cc_final: 0.8014 (m-30) REVERT: C 126 THR cc_start: 0.8918 (m) cc_final: 0.8682 (p) REVERT: C 173 ASN cc_start: 0.8549 (p0) cc_final: 0.7975 (t0) REVERT: D 65 GLN cc_start: 0.9178 (mt0) cc_final: 0.8910 (mt0) REVERT: D 150 GLU cc_start: 0.7840 (pp20) cc_final: 0.7265 (tp30) REVERT: E 173 ASN cc_start: 0.8464 (p0) cc_final: 0.7671 (t0) REVERT: F 12 ASN cc_start: 0.8028 (t0) cc_final: 0.7623 (m-40) REVERT: F 17 MET cc_start: 0.8853 (ttm) cc_final: 0.8615 (ttm) REVERT: F 53 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7198 (p0) REVERT: F 62 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8432 (mttp) REVERT: F 133 MET cc_start: 0.9276 (mtm) cc_final: 0.8985 (mtp) REVERT: F 150 GLU cc_start: 0.7974 (pp20) cc_final: 0.7081 (tp30) REVERT: G 68 LYS cc_start: 0.8226 (tttt) cc_final: 0.6415 (tptt) REVERT: H 38 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8630 (ptp-170) REVERT: H 81 MET cc_start: 0.9191 (ttp) cc_final: 0.8893 (ttt) REVERT: H 155 TYR cc_start: 0.6132 (p90) cc_final: 0.5514 (p90) REVERT: I 87 ASP cc_start: 0.8114 (t0) cc_final: 0.7896 (t0) REVERT: I 167 SER cc_start: 0.8264 (t) cc_final: 0.7988 (m) REVERT: J 180 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7196 (mm) REVERT: J 181 GLN cc_start: 0.7611 (tt0) cc_final: 0.6756 (mt0) REVERT: J 185 LEU cc_start: 0.8388 (mp) cc_final: 0.7804 (mt) REVERT: K 141 LEU cc_start: 0.6641 (mp) cc_final: 0.5945 (tt) REVERT: K 145 TYR cc_start: 0.7174 (t80) cc_final: 0.6702 (t80) REVERT: L 10 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: L 83 MET cc_start: 0.8369 (tpp) cc_final: 0.8050 (mmt) REVERT: L 181 GLN cc_start: 0.7700 (tt0) cc_final: 0.6748 (mt0) outliers start: 55 outliers final: 46 residues processed: 293 average time/residue: 0.6431 time to fit residues: 212.0275 Evaluate side-chains 301 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 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 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 208 ARG Chi-restraints excluded: chain E residue 262 THR 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 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 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 78 THR Chi-restraints excluded: chain J residue 24 VAL 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 3 GLN Chi-restraints excluded: chain L residue 10 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 176 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS I 81 GLN K 81 GLN L 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101833 restraints weight = 29870.346| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.54 r_work: 0.2836 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2415 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= 0.169 Angle : 0.668 17.874 30108 Z= 0.322 Chirality : 0.048 0.355 3507 Planarity : 0.004 0.041 3777 Dihedral : 8.082 59.339 3983 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.40 % Allowed : 16.86 % Favored : 80.74 % 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 aren not related in a simple way. whole: -0.06 (0.16), residues: 2670 helix: 2.80 (0.26), residues: 363 sheet: 0.12 (0.18), residues: 855 loop : -0.88 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 123 TYR 0.023 0.001 TYR A 100 PHE 0.015 0.002 PHE D 9 TRP 0.009 0.001 TRP J 50 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00394 (22008) covalent geometry : angle 0.63733 (29886) SS BOND : bond 0.00418 ( 30) SS BOND : angle 2.59813 ( 60) hydrogen bonds : bond 0.03447 ( 872) hydrogen bonds : angle 4.99625 ( 2319) link_ALPHA1-2 : bond 0.00112 ( 3) link_ALPHA1-2 : angle 1.69803 ( 9) link_ALPHA1-3 : bond 0.00622 ( 9) link_ALPHA1-3 : angle 2.87085 ( 27) link_ALPHA1-6 : bond 0.00610 ( 9) link_ALPHA1-6 : angle 1.99268 ( 27) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.54603 ( 45) link_NAG-ASN : bond 0.00580 ( 18) link_NAG-ASN : angle 2.85030 ( 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 311 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 0.749 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: 0.8447 (m-30) cc_final: 0.8235 (m-30) REVERT: A 104 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7845 (t0) REVERT: A 189 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8733 (tm-30) REVERT: B 11 GLU cc_start: 0.8067 (pp20) cc_final: 0.7838 (pp20) REVERT: B 17 MET cc_start: 0.8713 (ttm) cc_final: 0.7979 (ttm) REVERT: B 117 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8562 (mttm) REVERT: B 148 CYS cc_start: 0.6679 (t) cc_final: 0.6053 (t) REVERT: B 150 GLU cc_start: 0.7835 (pp20) cc_final: 0.6972 (tp30) REVERT: C 35 GLU cc_start: 0.8689 (tt0) cc_final: 0.8354 (tt0) REVERT: C 77 ASP cc_start: 0.8229 (m-30) cc_final: 0.8018 (m-30) REVERT: C 126 THR cc_start: 0.8910 (m) cc_final: 0.8669 (p) REVERT: C 173 ASN cc_start: 0.8543 (p0) cc_final: 0.7961 (t0) REVERT: D 150 GLU cc_start: 0.7836 (pp20) cc_final: 0.7279 (tp30) REVERT: E 173 ASN cc_start: 0.8433 (p0) cc_final: 0.7706 (t0) REVERT: F 12 ASN cc_start: 0.8041 (t0) cc_final: 0.7645 (m-40) REVERT: F 17 MET cc_start: 0.8860 (ttm) cc_final: 0.8641 (ttm) REVERT: F 53 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7208 (p0) REVERT: F 62 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8347 (mttp) REVERT: F 133 MET cc_start: 0.9284 (mtm) cc_final: 0.8993 (mtp) REVERT: F 150 GLU cc_start: 0.7965 (pp20) cc_final: 0.7079 (tp30) REVERT: G 16 GLN cc_start: 0.7039 (pm20) cc_final: 0.6690 (pm20) REVERT: G 68 LYS cc_start: 0.8223 (tttt) cc_final: 0.6419 (tptt) REVERT: H 38 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8341 (ptp-170) REVERT: H 65 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8114 (mm-40) REVERT: H 81 MET cc_start: 0.9177 (ttp) cc_final: 0.8869 (ttt) REVERT: H 83 MET cc_start: 0.8851 (mmt) cc_final: 0.8628 (mmt) REVERT: H 155 TYR cc_start: 0.6147 (p90) cc_final: 0.5660 (p90) REVERT: H 171 SER cc_start: 0.7688 (OUTLIER) cc_final: 0.7283 (p) REVERT: H 181 GLN cc_start: 0.7590 (tt0) cc_final: 0.7284 (mp-120) REVERT: I 87 ASP cc_start: 0.8204 (t0) cc_final: 0.7997 (t0) REVERT: J 181 GLN cc_start: 0.7603 (tt0) cc_final: 0.6728 (mt0) REVERT: J 185 LEU cc_start: 0.8391 (mp) cc_final: 0.7793 (mt) REVERT: K 107 LYS cc_start: 0.8508 (mtpm) cc_final: 0.8089 (mtpt) REVERT: K 141 LEU cc_start: 0.6732 (mp) cc_final: 0.5989 (tt) REVERT: K 145 TYR cc_start: 0.7143 (t80) cc_final: 0.6723 (t80) REVERT: L 10 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: L 55 ASP cc_start: 0.8971 (p0) cc_final: 0.8750 (p0) REVERT: L 83 MET cc_start: 0.8317 (tpp) cc_final: 0.8022 (mmt) REVERT: L 181 GLN cc_start: 0.7705 (tt0) cc_final: 0.6751 (mt0) outliers start: 56 outliers final: 45 residues processed: 290 average time/residue: 0.6592 time to fit residues: 214.5072 Evaluate side-chains 302 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 277 CYS 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 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 42 GLN 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 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 78 THR Chi-restraints excluded: chain J residue 24 VAL 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 190 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 205 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 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 = 0.3743 r_free = 0.3743 target = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100466 restraints weight = 29897.649| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.45 r_work: 0.2793 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22092 Z= 0.226 Angle : 0.702 18.535 30108 Z= 0.341 Chirality : 0.049 0.387 3507 Planarity : 0.005 0.050 3777 Dihedral : 8.230 57.528 3983 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.35 % Allowed : 16.90 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.12 (0.16), residues: 2670 helix: 2.63 (0.26), residues: 366 sheet: 0.11 (0.18), residues: 855 loop : -0.92 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 123 TYR 0.026 0.002 TYR A 100 PHE 0.016 0.002 PHE F 9 TRP 0.011 0.002 TRP B 92 HIS 0.006 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00532 (22008) covalent geometry : angle 0.67066 (29886) SS BOND : bond 0.00444 ( 30) SS BOND : angle 2.85774 ( 60) hydrogen bonds : bond 0.03663 ( 872) hydrogen bonds : angle 5.08615 ( 2319) link_ALPHA1-2 : bond 0.00080 ( 3) link_ALPHA1-2 : angle 1.73080 ( 9) link_ALPHA1-3 : bond 0.00546 ( 9) link_ALPHA1-3 : angle 2.92536 ( 27) link_ALPHA1-6 : bond 0.00548 ( 9) link_ALPHA1-6 : angle 1.99748 ( 27) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 1.68829 ( 45) link_NAG-ASN : bond 0.00759 ( 18) link_NAG-ASN : angle 2.73209 ( 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 309 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 0.832 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: 0.8443 (m-30) cc_final: 0.8217 (m-30) REVERT: A 104 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7869 (t0) REVERT: B 17 MET cc_start: 0.8710 (ttm) cc_final: 0.7966 (ttm) REVERT: B 117 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8528 (mttm) REVERT: B 148 CYS cc_start: 0.6793 (t) cc_final: 0.6168 (t) REVERT: B 150 GLU cc_start: 0.7890 (pp20) cc_final: 0.7009 (tp30) REVERT: C 35 GLU cc_start: 0.8665 (tt0) cc_final: 0.8340 (tt0) REVERT: C 77 ASP cc_start: 0.8262 (m-30) cc_final: 0.8028 (m-30) REVERT: C 173 ASN cc_start: 0.8566 (p0) cc_final: 0.7930 (t0) REVERT: D 150 GLU cc_start: 0.7866 (pp20) cc_final: 0.7308 (tp30) REVERT: E 173 ASN cc_start: 0.8457 (p0) cc_final: 0.7733 (t0) REVERT: F 12 ASN cc_start: 0.8069 (t0) cc_final: 0.7661 (m-40) REVERT: F 17 MET cc_start: 0.8866 (ttm) cc_final: 0.8652 (ttm) REVERT: F 53 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7038 (p0) REVERT: F 62 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8496 (mttp) REVERT: F 133 MET cc_start: 0.9330 (mtm) cc_final: 0.9044 (mtp) REVERT: F 150 GLU cc_start: 0.7947 (pp20) cc_final: 0.7080 (tp30) REVERT: G 16 GLN cc_start: 0.7109 (pm20) cc_final: 0.6829 (pm20) REVERT: H 38 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8627 (ptp-170) REVERT: H 65 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8136 (mm-40) REVERT: H 81 MET cc_start: 0.9218 (ttp) cc_final: 0.8892 (ttt) REVERT: H 83 MET cc_start: 0.8862 (mmt) cc_final: 0.8639 (mmt) REVERT: H 155 TYR cc_start: 0.6146 (p90) cc_final: 0.5611 (p90) REVERT: H 179 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8216 (t) REVERT: H 181 GLN cc_start: 0.7581 (tt0) cc_final: 0.7261 (mp-120) REVERT: I 87 ASP cc_start: 0.8217 (t0) cc_final: 0.7972 (t0) REVERT: I 129 GLN cc_start: 0.4747 (tm-30) cc_final: 0.4535 (tt0) REVERT: J 181 GLN cc_start: 0.7589 (tt0) cc_final: 0.6698 (mt0) REVERT: J 185 LEU cc_start: 0.8386 (mp) cc_final: 0.7761 (mt) REVERT: K 107 LYS cc_start: 0.8506 (mtpm) cc_final: 0.8056 (mtpt) REVERT: K 141 LEU cc_start: 0.6719 (mp) cc_final: 0.5983 (tt) REVERT: K 145 TYR cc_start: 0.7176 (t80) cc_final: 0.6725 (t80) REVERT: L 10 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: L 83 MET cc_start: 0.8372 (tpp) cc_final: 0.8058 (mmt) REVERT: L 181 GLN cc_start: 0.7711 (tt0) cc_final: 0.6745 (mt0) outliers start: 55 outliers final: 44 residues processed: 288 average time/residue: 0.6387 time to fit residues: 206.8183 Evaluate side-chains 299 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 196 VAL 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 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER 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 42 GLN 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 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 H residue 179 VAL 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 190 SER Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 160 optimal weight: 0.0970 chunk 164 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN H 165 ASN 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 = 0.3771 r_free = 0.3771 target = 0.147227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103221 restraints weight = 29812.430| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.53 r_work: 0.2832 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22092 Z= 0.130 Angle : 0.643 15.322 30108 Z= 0.312 Chirality : 0.047 0.354 3507 Planarity : 0.004 0.051 3777 Dihedral : 7.717 55.650 3983 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.18 % Allowed : 17.20 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.00 (0.16), residues: 2670 helix: 2.92 (0.26), residues: 363 sheet: 0.16 (0.18), residues: 855 loop : -0.87 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 123 TYR 0.024 0.001 TYR A 100 PHE 0.014 0.001 PHE B 3 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00300 (22008) covalent geometry : angle 0.61429 (29886) SS BOND : bond 0.00281 ( 30) SS BOND : angle 2.56027 ( 60) hydrogen bonds : bond 0.03269 ( 872) hydrogen bonds : angle 4.89518 ( 2319) link_ALPHA1-2 : bond 0.00194 ( 3) link_ALPHA1-2 : angle 1.61595 ( 9) link_ALPHA1-3 : bond 0.00726 ( 9) link_ALPHA1-3 : angle 2.74031 ( 27) link_ALPHA1-6 : bond 0.00632 ( 9) link_ALPHA1-6 : angle 1.89546 ( 27) link_BETA1-4 : bond 0.00336 ( 15) link_BETA1-4 : angle 1.38897 ( 45) link_NAG-ASN : bond 0.00647 ( 18) link_NAG-ASN : angle 2.57595 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9470.09 seconds wall clock time: 161 minutes 44.69 seconds (9704.69 seconds total)