Starting phenix.real_space_refine on Wed Jun 18 21:42:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k39_22653/06_2025/7k39_22653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k39_22653/06_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_22653/06_2025/7k39_22653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k39_22653/06_2025/7k39_22653.map" model { file = "/net/cci-nas-00/data/ceres_data/7k39_22653/06_2025/7k39_22653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k39_22653/06_2025/7k39_22653.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.64, per 1000 atoms: 0.91 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: 8.34 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 3.58 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: 13.15 Time building geometry restraints manager: 9.42 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: 0.12 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: 12.060 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: 0.030 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 73.480 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.140 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:16.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.090 ------------------------------------------------------------------------------- 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 : 8.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (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 TRP 0.013 0.002 TRP H 50 HIS 0.004 0.001 HIS C 18 PHE 0.024 0.002 PHE F 3 TYR 0.018 0.002 TYR I 178 ARG 0.006 0.000 ARG G 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 18) link_NAG-ASN : angle 3.09130 ( 54) 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_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) hydrogen bonds : bond 0.13969 ( 872) hydrogen bonds : angle 7.01230 ( 2319) SS BOND : bond 0.03604 ( 30) SS BOND : angle 2.18695 ( 60) covalent geometry : bond 0.00747 (22008) covalent geometry : angle 0.78359 (29886) *********************** 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 : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7923 (m-30) cc_final: 0.7606 (m-30) REVERT: A 45 SER cc_start: 0.9230 (p) cc_final: 0.8876 (t) REVERT: A 189 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 190 GLU cc_start: 0.8549 (tt0) cc_final: 0.8349 (tt0) REVERT: A 268 MET cc_start: 0.9011 (ttm) cc_final: 0.8750 (ttm) REVERT: A 280 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7848 (tp30) REVERT: B 17 MET cc_start: 0.8411 (tpp) cc_final: 0.8133 (ttm) REVERT: B 76 ARG cc_start: 0.8565 (mtp180) cc_final: 0.8089 (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: 0.7631 (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: 1.5210 time to fit residues: 701.3893 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 : 2.339 ------------------------------------------------------------------------------- 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 225 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 136 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 0.0060 chunk 80 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- 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 E 191 GLN 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 91 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103325 restraints weight = 30003.684| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.49 r_work: 0.2835 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22092 Z= 0.128 Angle : 0.658 9.260 30108 Z= 0.318 Chirality : 0.048 0.369 3507 Planarity : 0.004 0.039 3777 Dihedral : 10.502 76.116 3983 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.48 % Allowed : 8.52 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2670 helix: 2.61 (0.26), residues: 363 sheet: -0.02 (0.18), residues: 801 loop : -1.06 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS D 106 PHE 0.011 0.001 PHE J 156 TYR 0.018 0.001 TYR A 100 ARG 0.006 0.001 ARG G 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 18) link_NAG-ASN : angle 2.68855 ( 54) link_ALPHA1-6 : bond 0.00440 ( 9) link_ALPHA1-6 : angle 2.60817 ( 27) link_BETA1-4 : bond 0.00269 ( 15) link_BETA1-4 : angle 2.04284 ( 45) link_ALPHA1-2 : bond 0.00183 ( 3) link_ALPHA1-2 : angle 1.94851 ( 9) link_ALPHA1-3 : bond 0.00360 ( 9) link_ALPHA1-3 : angle 3.23224 ( 27) hydrogen bonds : bond 0.03647 ( 872) hydrogen bonds : angle 5.65265 ( 2319) SS BOND : bond 0.00993 ( 30) SS BOND : angle 1.28985 ( 60) covalent geometry : bond 0.00279 (22008) covalent geometry : angle 0.62968 (29886) *********************** 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 349 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 2.376 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 15 LEU cc_start: 0.9166 (mp) cc_final: 0.8899 (mt) REVERT: A 31 ASP cc_start: 0.8424 (m-30) cc_final: 0.8206 (m-30) REVERT: A 189 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8651 (tm-30) REVERT: A 280 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8669 (mm-30) REVERT: B 121 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8753 (ttpt) REVERT: C 35 GLU cc_start: 0.8646 (tt0) cc_final: 0.8289 (tt0) REVERT: C 77 ASP cc_start: 0.8246 (m-30) cc_final: 0.7979 (m-30) REVERT: C 173 ASN cc_start: 0.8572 (p0) cc_final: 0.8153 (t0) REVERT: C 307 LYS cc_start: 0.8953 (mttp) cc_final: 0.8510 (mmtt) REVERT: D 17 MET cc_start: 0.8548 (tpp) cc_final: 0.7944 (ttm) REVERT: D 65 GLN cc_start: 0.9199 (mt0) cc_final: 0.8894 (mt0) REVERT: D 150 GLU cc_start: 0.7754 (pp20) cc_final: 0.6757 (tm-30) REVERT: E 31 ASP cc_start: 0.8412 (m-30) cc_final: 0.8093 (m-30) REVERT: E 40 THR cc_start: 0.9365 (t) cc_final: 0.9129 (p) REVERT: E 189 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8667 (tp40) REVERT: F 17 MET cc_start: 0.8757 (ttm) cc_final: 0.8392 (ttm) REVERT: F 47 GLN cc_start: 0.8984 (mt0) cc_final: 0.8592 (mt0) REVERT: F 115 MET cc_start: 0.9131 (tpt) cc_final: 0.8860 (tpt) REVERT: F 133 MET cc_start: 0.9254 (mtm) cc_final: 0.8971 (mtm) REVERT: F 150 GLU cc_start: 0.7838 (pp20) cc_final: 0.7082 (tp30) REVERT: G 16 GLN cc_start: 0.7213 (pm20) cc_final: 0.6924 (pm20) REVERT: H 81 MET cc_start: 0.9179 (ttp) cc_final: 0.8877 (ttt) REVERT: H 155 TYR cc_start: 0.6160 (p90) cc_final: 0.5229 (p90) REVERT: H 181 GLN cc_start: 0.7523 (tt0) cc_final: 0.6828 (mt0) REVERT: I 55 ASN cc_start: 0.8268 (t0) cc_final: 0.8046 (t0) REVERT: I 91 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: I 167 SER cc_start: 0.8140 (t) cc_final: 0.7719 (m) REVERT: J 181 GLN cc_start: 0.7707 (tt0) cc_final: 0.6820 (mt0) REVERT: J 185 LEU cc_start: 0.8340 (mp) cc_final: 0.7803 (mt) REVERT: J 219 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6023 (tppt) REVERT: K 145 TYR cc_start: 0.7028 (t80) cc_final: 0.6531 (t80) REVERT: L 13 LYS cc_start: 0.8993 (ttpt) cc_final: 0.8721 (mptm) REVERT: L 59 LYS cc_start: 0.8929 (tptp) cc_final: 0.8679 (tptm) REVERT: L 127 LYS cc_start: 0.8393 (tppt) cc_final: 0.8003 (mmmm) REVERT: L 181 GLN cc_start: 0.7782 (tt0) cc_final: 0.6549 (mt0) outliers start: 58 outliers final: 29 residues processed: 319 average time/residue: 1.5318 time to fit residues: 547.4197 Evaluate side-chains 284 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 321 ARG Chi-restraints excluded: chain E residue 323 VAL 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 91 GLN Chi-restraints excluded: chain I residue 107 LYS 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 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 206 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 232 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 125 GLN G 39 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 = 0.3757 r_free = 0.3757 target = 0.145909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101968 restraints weight = 29811.471| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.52 r_work: 0.2825 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22092 Z= 0.169 Angle : 0.643 11.321 30108 Z= 0.312 Chirality : 0.048 0.382 3507 Planarity : 0.004 0.040 3777 Dihedral : 10.073 72.181 3983 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.70 % Allowed : 11.00 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2670 helix: 2.35 (0.27), residues: 381 sheet: 0.11 (0.18), residues: 807 loop : -0.98 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 37 HIS 0.008 0.001 HIS I 36 PHE 0.015 0.002 PHE D 9 TYR 0.017 0.001 TYR A 100 ARG 0.006 0.000 ARG L 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00879 ( 18) link_NAG-ASN : angle 2.61685 ( 54) link_ALPHA1-6 : bond 0.00488 ( 9) link_ALPHA1-6 : angle 2.22052 ( 27) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 1.82360 ( 45) link_ALPHA1-2 : bond 0.00104 ( 3) link_ALPHA1-2 : angle 1.74693 ( 9) link_ALPHA1-3 : bond 0.00442 ( 9) link_ALPHA1-3 : angle 2.94470 ( 27) hydrogen bonds : bond 0.03629 ( 872) hydrogen bonds : angle 5.41657 ( 2319) SS BOND : bond 0.00586 ( 30) SS BOND : angle 1.30266 ( 60) covalent geometry : bond 0.00391 (22008) covalent geometry : angle 0.61798 (29886) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 2.501 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: 0.8432 (m-30) cc_final: 0.8227 (m-30) REVERT: A 104 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7936 (t0) REVERT: A 189 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8677 (tm-30) REVERT: A 280 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8501 (tp30) REVERT: B 17 MET cc_start: 0.8534 (ttm) cc_final: 0.8048 (ttm) REVERT: B 121 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8766 (ttpt) REVERT: C 35 GLU cc_start: 0.8655 (tt0) cc_final: 0.8330 (tt0) REVERT: C 77 ASP cc_start: 0.8277 (m-30) cc_final: 0.8003 (m-30) REVERT: C 173 ASN cc_start: 0.8583 (p0) cc_final: 0.8056 (t0) REVERT: C 307 LYS cc_start: 0.8922 (mttp) cc_final: 0.8590 (mmtt) REVERT: D 17 MET cc_start: 0.8470 (tpp) cc_final: 0.8079 (ttm) REVERT: D 65 GLN cc_start: 0.9195 (mt0) cc_final: 0.8912 (mt0) REVERT: D 150 GLU cc_start: 0.7816 (pp20) cc_final: 0.6889 (tm-30) REVERT: E 31 ASP cc_start: 0.8512 (m-30) cc_final: 0.8167 (m-30) REVERT: E 32 ASP cc_start: 0.8523 (m-30) cc_final: 0.8253 (m-30) REVERT: E 40 THR cc_start: 0.9398 (t) cc_final: 0.9152 (p) REVERT: E 189 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8691 (tp40) REVERT: F 17 MET cc_start: 0.8722 (ttm) cc_final: 0.8388 (ttm) REVERT: F 47 GLN cc_start: 0.8907 (mt0) cc_final: 0.8679 (mt0) REVERT: F 133 MET cc_start: 0.9291 (mtm) cc_final: 0.9008 (mtp) REVERT: F 150 GLU cc_start: 0.7856 (pp20) cc_final: 0.7110 (tp30) REVERT: G 16 GLN cc_start: 0.7220 (pm20) cc_final: 0.6998 (pm20) REVERT: G 39 GLN cc_start: 0.8867 (tt0) cc_final: 0.8626 (pt0) REVERT: H 38 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8328 (ptp-170) REVERT: H 81 MET cc_start: 0.9190 (ttp) cc_final: 0.8907 (ttt) REVERT: H 90 ASP cc_start: 0.8210 (m-30) cc_final: 0.7985 (m-30) REVERT: H 155 TYR cc_start: 0.6167 (p90) cc_final: 0.5302 (p90) REVERT: H 181 GLN cc_start: 0.7524 (tt0) cc_final: 0.6949 (mt0) REVERT: I 167 SER cc_start: 0.8284 (t) cc_final: 0.7873 (m) REVERT: J 3 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8887 (mm-40) REVERT: J 181 GLN cc_start: 0.7738 (tt0) cc_final: 0.6867 (mt0) REVERT: J 185 LEU cc_start: 0.8404 (mp) cc_final: 0.7870 (mt) REVERT: K 107 LYS cc_start: 0.8701 (mtpm) cc_final: 0.8293 (mtpt) REVERT: K 145 TYR cc_start: 0.7217 (t80) cc_final: 0.6788 (t80) REVERT: L 10 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: L 54 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7430 (t80) REVERT: L 83 MET cc_start: 0.8665 (tpp) cc_final: 0.8119 (mmt) REVERT: L 181 GLN cc_start: 0.7748 (tt0) cc_final: 0.6645 (mt0) outliers start: 63 outliers final: 40 residues processed: 301 average time/residue: 1.5470 time to fit residues: 525.5789 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 : 2.353 ------------------------------------------------------------------------------- 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 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 86 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 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 73 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER 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 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 107 LYS Chi-restraints excluded: chain J residue 3 GLN 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 10 GLU Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 128 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** C 197 GLN D 47 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** 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** J 174 HIS ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099282 restraints weight = 30154.564| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.63 r_work: 0.2794 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22092 Z= 0.260 Angle : 0.689 9.742 30108 Z= 0.335 Chirality : 0.050 0.325 3507 Planarity : 0.004 0.041 3777 Dihedral : 9.830 69.214 3983 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.91 % Allowed : 12.67 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2670 helix: 2.14 (0.27), residues: 381 sheet: 0.02 (0.18), residues: 819 loop : -1.02 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 92 HIS 0.009 0.001 HIS K 36 PHE 0.017 0.002 PHE D 9 TYR 0.017 0.002 TYR A 100 ARG 0.007 0.001 ARG E 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 18) link_NAG-ASN : angle 2.74013 ( 54) link_ALPHA1-6 : bond 0.00516 ( 9) link_ALPHA1-6 : angle 2.22169 ( 27) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 1.98504 ( 45) link_ALPHA1-2 : bond 0.00054 ( 3) link_ALPHA1-2 : angle 1.80598 ( 9) link_ALPHA1-3 : bond 0.00439 ( 9) link_ALPHA1-3 : angle 3.02983 ( 27) hydrogen bonds : bond 0.03887 ( 872) hydrogen bonds : angle 5.42988 ( 2319) SS BOND : bond 0.00546 ( 30) SS BOND : angle 1.37202 ( 60) covalent geometry : bond 0.00613 (22008) covalent geometry : angle 0.66476 (29886) *********************** 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 329 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 261 time to evaluate : 2.334 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: 0.8443 (m-30) cc_final: 0.8210 (m-30) REVERT: A 104 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7966 (t0) REVERT: A 189 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 17 MET cc_start: 0.8604 (ttm) cc_final: 0.7861 (ttm) REVERT: B 110 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8970 (tp) REVERT: C 35 GLU cc_start: 0.8619 (tt0) cc_final: 0.8304 (tt0) REVERT: C 77 ASP cc_start: 0.8342 (m-30) cc_final: 0.8084 (m-30) REVERT: C 173 ASN cc_start: 0.8617 (p0) cc_final: 0.7993 (t0) REVERT: D 17 MET cc_start: 0.8465 (tpp) cc_final: 0.8072 (ttm) REVERT: D 32 THR cc_start: 0.8575 (m) cc_final: 0.8373 (p) REVERT: D 150 GLU cc_start: 0.7859 (pp20) cc_final: 0.7029 (tm-30) REVERT: E 31 ASP cc_start: 0.8531 (m-30) cc_final: 0.8207 (m-30) REVERT: E 32 ASP cc_start: 0.8651 (m-30) cc_final: 0.8381 (m-30) REVERT: E 40 THR cc_start: 0.9387 (t) cc_final: 0.9154 (p) REVERT: E 189 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8695 (tm-30) REVERT: E 210 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8788 (pt0) REVERT: F 17 MET cc_start: 0.8815 (ttm) cc_final: 0.8561 (ttm) REVERT: F 62 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8654 (mttp) REVERT: F 71 SER cc_start: 0.9323 (m) cc_final: 0.9122 (p) REVERT: F 121 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8591 (tttm) REVERT: F 133 MET cc_start: 0.9309 (mtm) cc_final: 0.8999 (mtp) REVERT: G 81 GLN cc_start: 0.7833 (pm20) cc_final: 0.7607 (pm20) REVERT: H 38 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8403 (ptp-170) REVERT: H 81 MET cc_start: 0.9213 (ttp) cc_final: 0.8926 (ttt) REVERT: H 87 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7627 (mtp85) REVERT: H 155 TYR cc_start: 0.6155 (p90) cc_final: 0.5230 (p90) REVERT: I 22 CYS cc_start: 0.7297 (t) cc_final: 0.6910 (t) REVERT: I 167 SER cc_start: 0.8272 (t) cc_final: 0.7890 (m) REVERT: J 155 TYR cc_start: 0.6406 (p90) cc_final: 0.6194 (p90) REVERT: J 181 GLN cc_start: 0.7733 (tt0) cc_final: 0.6844 (mt0) REVERT: J 185 LEU cc_start: 0.8393 (mp) cc_final: 0.7856 (mt) REVERT: J 219 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6094 (tppt) REVERT: K 107 LYS cc_start: 0.8685 (mtpm) cc_final: 0.8288 (mtpt) REVERT: K 145 TYR cc_start: 0.7221 (t80) cc_final: 0.6763 (t80) REVERT: L 10 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: L 83 MET cc_start: 0.8619 (tpp) cc_final: 0.8170 (mmt) REVERT: L 181 GLN cc_start: 0.7748 (tt0) cc_final: 0.6646 (mt0) outliers start: 68 outliers final: 42 residues processed: 300 average time/residue: 1.4061 time to fit residues: 476.4841 Evaluate side-chains 301 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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 86 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 210 GLN 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 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 87 ARG 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 219 LYS Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 190 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 246 optimal weight: 0.2980 chunk 137 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 HIS ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100621 restraints weight = 29866.101| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.57 r_work: 0.2765 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 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 = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2037 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= 0.181 Angle : 0.645 11.369 30108 Z= 0.311 Chirality : 0.048 0.365 3507 Planarity : 0.004 0.045 3777 Dihedral : 9.228 62.654 3983 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.65 % Allowed : 14.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2670 helix: 2.26 (0.27), residues: 381 sheet: 0.06 (0.18), residues: 825 loop : -1.00 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 50 HIS 0.004 0.001 HIS D 106 PHE 0.015 0.002 PHE D 9 TYR 0.018 0.001 TYR F 162 ARG 0.008 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 18) link_NAG-ASN : angle 2.79806 ( 54) link_ALPHA1-6 : bond 0.00542 ( 9) link_ALPHA1-6 : angle 2.18451 ( 27) link_BETA1-4 : bond 0.00309 ( 15) link_BETA1-4 : angle 1.73855 ( 45) link_ALPHA1-2 : bond 0.00110 ( 3) link_ALPHA1-2 : angle 1.69294 ( 9) link_ALPHA1-3 : bond 0.00513 ( 9) link_ALPHA1-3 : angle 2.95855 ( 27) hydrogen bonds : bond 0.03561 ( 872) hydrogen bonds : angle 5.22393 ( 2319) SS BOND : bond 0.00476 ( 30) SS BOND : angle 1.52678 ( 60) covalent geometry : bond 0.00421 (22008) covalent geometry : angle 0.61843 (29886) *********************** 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 323 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8446 (m-30) cc_final: 0.8236 (m-30) REVERT: A 104 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7952 (t0) REVERT: A 189 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8645 (tm-30) REVERT: B 17 MET cc_start: 0.8749 (ttm) cc_final: 0.8001 (ttm) REVERT: B 150 GLU cc_start: 0.7791 (pp20) cc_final: 0.6990 (tp30) REVERT: C 35 GLU cc_start: 0.8726 (tt0) cc_final: 0.8374 (tt0) REVERT: C 77 ASP cc_start: 0.8238 (m-30) cc_final: 0.7990 (m-30) REVERT: C 173 ASN cc_start: 0.8563 (p0) cc_final: 0.8003 (t0) REVERT: D 12 ASN cc_start: 0.7946 (t0) cc_final: 0.7467 (t0) REVERT: D 17 MET cc_start: 0.8277 (tpp) cc_final: 0.8026 (ttm) REVERT: D 150 GLU cc_start: 0.7765 (pp20) cc_final: 0.6939 (tm-30) REVERT: E 32 ASP cc_start: 0.8592 (m-30) cc_final: 0.8316 (m-30) REVERT: E 40 THR cc_start: 0.9329 (t) cc_final: 0.9109 (p) REVERT: E 173 ASN cc_start: 0.8572 (p0) cc_final: 0.7503 (t0) REVERT: E 189 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8329 (tm-30) REVERT: F 12 ASN cc_start: 0.8051 (t0) cc_final: 0.7365 (t0) REVERT: F 17 MET cc_start: 0.8775 (ttm) cc_final: 0.8548 (ttm) REVERT: F 121 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8499 (tttm) REVERT: F 133 MET cc_start: 0.9287 (mtm) cc_final: 0.8958 (mtp) REVERT: G 16 GLN cc_start: 0.7101 (pm20) cc_final: 0.6810 (pm20) REVERT: G 39 GLN cc_start: 0.8869 (tt0) cc_final: 0.8532 (tt0) REVERT: G 81 GLN cc_start: 0.7712 (pm20) cc_final: 0.7467 (pm20) REVERT: H 38 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8263 (ptp-170) REVERT: H 81 MET cc_start: 0.9221 (ttp) cc_final: 0.8937 (ttt) REVERT: H 155 TYR cc_start: 0.6049 (p90) cc_final: 0.5195 (p90) REVERT: I 55 ASN cc_start: 0.7346 (t0) cc_final: 0.7124 (t0) REVERT: I 167 SER cc_start: 0.8204 (t) cc_final: 0.7776 (p) REVERT: J 180 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7046 (mm) REVERT: J 181 GLN cc_start: 0.7655 (tt0) cc_final: 0.6714 (mt0) REVERT: J 185 LEU cc_start: 0.8296 (mp) cc_final: 0.7687 (mt) REVERT: K 107 LYS cc_start: 0.8584 (mtpm) cc_final: 0.8183 (mtpt) REVERT: K 141 LEU cc_start: 0.6368 (mp) cc_final: 0.5650 (tt) REVERT: K 145 TYR cc_start: 0.7267 (t80) cc_final: 0.6686 (t80) REVERT: L 10 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: L 83 MET cc_start: 0.8540 (tpp) cc_final: 0.8123 (mmt) REVERT: L 181 GLN cc_start: 0.7757 (tt0) cc_final: 0.6642 (mt0) outliers start: 62 outliers final: 43 residues processed: 296 average time/residue: 1.4294 time to fit residues: 479.0073 Evaluate side-chains 294 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 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 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 77 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 7 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101434 restraints weight = 29748.666| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.56 r_work: 0.2782 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22092 Z= 0.160 Angle : 0.644 16.886 30108 Z= 0.311 Chirality : 0.048 0.402 3507 Planarity : 0.004 0.041 3777 Dihedral : 8.795 58.650 3983 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.04 % Allowed : 14.93 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2670 helix: 2.67 (0.26), residues: 363 sheet: 0.06 (0.18), residues: 837 loop : -0.97 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 50 HIS 0.004 0.001 HIS D 106 PHE 0.015 0.002 PHE B 3 TYR 0.018 0.001 TYR F 162 ARG 0.008 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 18) link_NAG-ASN : angle 2.61959 ( 54) link_ALPHA1-6 : bond 0.00560 ( 9) link_ALPHA1-6 : angle 2.13816 ( 27) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 1.62213 ( 45) link_ALPHA1-2 : bond 0.00094 ( 3) link_ALPHA1-2 : angle 1.71419 ( 9) link_ALPHA1-3 : bond 0.00554 ( 9) link_ALPHA1-3 : angle 2.90873 ( 27) hydrogen bonds : bond 0.03447 ( 872) hydrogen bonds : angle 5.10352 ( 2319) SS BOND : bond 0.00488 ( 30) SS BOND : angle 2.39126 ( 60) covalent geometry : bond 0.00370 (22008) covalent geometry : angle 0.61476 (29886) *********************** 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 326 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 255 time to evaluate : 2.322 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: 0.8488 (m-30) cc_final: 0.8275 (m-30) REVERT: A 189 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8698 (tm-30) REVERT: B 17 MET cc_start: 0.8701 (ttm) cc_final: 0.7994 (ttm) REVERT: B 150 GLU cc_start: 0.7827 (pp20) cc_final: 0.6981 (tp30) REVERT: C 35 GLU cc_start: 0.8659 (tt0) cc_final: 0.8340 (tt0) REVERT: C 77 ASP cc_start: 0.8239 (m-30) cc_final: 0.8009 (m-30) REVERT: C 173 ASN cc_start: 0.8560 (p0) cc_final: 0.8029 (t0) REVERT: C 260 MET cc_start: 0.9221 (mtp) cc_final: 0.8988 (mtp) REVERT: D 12 ASN cc_start: 0.7943 (t0) cc_final: 0.7542 (t0) REVERT: D 150 GLU cc_start: 0.7784 (pp20) cc_final: 0.6782 (tp30) REVERT: E 32 ASP cc_start: 0.8596 (m-30) cc_final: 0.8361 (m-30) REVERT: E 40 THR cc_start: 0.9367 (t) cc_final: 0.9149 (p) REVERT: E 173 ASN cc_start: 0.8496 (p0) cc_final: 0.7614 (t0) REVERT: E 189 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8737 (tm130) REVERT: F 12 ASN cc_start: 0.8067 (t0) cc_final: 0.7397 (t0) REVERT: F 17 MET cc_start: 0.8834 (ttm) cc_final: 0.8603 (ttm) REVERT: F 53 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.7051 (p0) REVERT: F 62 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8337 (mttp) REVERT: F 123 ARG cc_start: 0.8898 (ttp-170) cc_final: 0.8665 (ttp80) REVERT: F 133 MET cc_start: 0.9286 (mtm) cc_final: 0.8977 (mtp) REVERT: G 16 GLN cc_start: 0.7251 (pm20) cc_final: 0.6984 (pm20) REVERT: G 39 GLN cc_start: 0.8878 (tt0) cc_final: 0.8569 (tt0) REVERT: G 81 GLN cc_start: 0.7793 (pm20) cc_final: 0.7321 (pm20) REVERT: H 38 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8609 (ptp-170) REVERT: H 81 MET cc_start: 0.9198 (ttp) cc_final: 0.8921 (ttt) REVERT: H 155 TYR cc_start: 0.6082 (p90) cc_final: 0.5280 (p90) REVERT: I 167 SER cc_start: 0.8227 (t) cc_final: 0.7805 (p) REVERT: J 38 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7825 (ptp-170) REVERT: J 90 ASP cc_start: 0.8462 (m-30) cc_final: 0.8228 (m-30) REVERT: J 180 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7149 (mm) REVERT: J 181 GLN cc_start: 0.7670 (tt0) cc_final: 0.6724 (mt0) REVERT: J 185 LEU cc_start: 0.8342 (mp) cc_final: 0.7759 (mt) REVERT: K 107 LYS cc_start: 0.8477 (mtpm) cc_final: 0.8046 (mtpt) REVERT: K 141 LEU cc_start: 0.6612 (mp) cc_final: 0.5865 (tt) REVERT: K 145 TYR cc_start: 0.7404 (t80) cc_final: 0.6840 (t80) REVERT: L 10 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: L 83 MET cc_start: 0.8502 (tpp) cc_final: 0.8145 (mmt) REVERT: L 181 GLN cc_start: 0.7667 (tt0) cc_final: 0.6707 (mt0) outliers start: 71 outliers final: 48 residues processed: 295 average time/residue: 1.4850 time to fit residues: 498.7378 Evaluate side-chains 300 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 4.812 ------------------------------------------------------------------------------- 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 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 196 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 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 82 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 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 258 optimal weight: 0.0050 chunk 159 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 150 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN ** I 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102888 restraints weight = 29718.321| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.47 r_work: 0.2850 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22092 Z= 0.131 Angle : 0.635 19.649 30108 Z= 0.306 Chirality : 0.047 0.336 3507 Planarity : 0.004 0.041 3777 Dihedral : 8.167 59.982 3983 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.61 % Allowed : 15.49 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2670 helix: 2.83 (0.26), residues: 363 sheet: 0.05 (0.18), residues: 855 loop : -0.86 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 174 PHE 0.013 0.001 PHE D 9 TYR 0.019 0.001 TYR F 162 ARG 0.012 0.000 ARG L 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 18) link_NAG-ASN : angle 2.58951 ( 54) link_ALPHA1-6 : bond 0.00596 ( 9) link_ALPHA1-6 : angle 2.01773 ( 27) link_BETA1-4 : bond 0.00329 ( 15) link_BETA1-4 : angle 1.46833 ( 45) link_ALPHA1-2 : bond 0.00153 ( 3) link_ALPHA1-2 : angle 1.67088 ( 9) link_ALPHA1-3 : bond 0.00669 ( 9) link_ALPHA1-3 : angle 2.83294 ( 27) hydrogen bonds : bond 0.03294 ( 872) hydrogen bonds : angle 4.94908 ( 2319) SS BOND : bond 0.00312 ( 30) SS BOND : angle 2.47548 ( 60) covalent geometry : bond 0.00299 (22008) covalent geometry : angle 0.60562 (29886) *********************** 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 326 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 3.274 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: 0.8435 (m-30) cc_final: 0.8213 (m-30) REVERT: A 189 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8696 (tm-30) REVERT: B 17 MET cc_start: 0.8706 (ttm) cc_final: 0.7993 (ttm) REVERT: B 150 GLU cc_start: 0.7876 (pp20) cc_final: 0.7116 (tp30) REVERT: C 35 GLU cc_start: 0.8627 (tt0) cc_final: 0.8307 (tt0) REVERT: C 173 ASN cc_start: 0.8542 (p0) cc_final: 0.8036 (t0) REVERT: D 12 ASN cc_start: 0.7958 (t0) cc_final: 0.7540 (t0) REVERT: D 150 GLU cc_start: 0.7795 (pp20) cc_final: 0.6832 (tp30) REVERT: E 32 ASP cc_start: 0.8543 (m-30) cc_final: 0.8342 (m-30) REVERT: E 173 ASN cc_start: 0.8451 (p0) cc_final: 0.7703 (t0) REVERT: F 12 ASN cc_start: 0.8047 (t0) cc_final: 0.7606 (t0) REVERT: F 17 MET cc_start: 0.8866 (ttm) cc_final: 0.8645 (ttm) REVERT: F 123 ARG cc_start: 0.8875 (ttp-170) cc_final: 0.8556 (ttp80) REVERT: F 133 MET cc_start: 0.9269 (mtm) cc_final: 0.8965 (mtp) REVERT: G 81 GLN cc_start: 0.8128 (pm20) cc_final: 0.7810 (pm20) REVERT: H 65 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8170 (mm-40) REVERT: H 81 MET cc_start: 0.9172 (ttp) cc_final: 0.8905 (ttt) REVERT: H 155 TYR cc_start: 0.6124 (p90) cc_final: 0.5494 (p90) REVERT: H 171 SER cc_start: 0.7695 (OUTLIER) cc_final: 0.7288 (p) REVERT: I 87 ASP cc_start: 0.8138 (t0) cc_final: 0.7893 (t0) REVERT: J 38 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.7797 (ptp-170) REVERT: J 90 ASP cc_start: 0.8472 (m-30) cc_final: 0.8250 (m-30) REVERT: J 180 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7244 (mm) REVERT: J 181 GLN cc_start: 0.7617 (tt0) cc_final: 0.6756 (mt0) REVERT: J 185 LEU cc_start: 0.8384 (mp) cc_final: 0.7796 (mt) REVERT: K 107 LYS cc_start: 0.8467 (mtpm) cc_final: 0.8045 (mtpt) REVERT: K 141 LEU cc_start: 0.6680 (mp) cc_final: 0.5935 (tt) REVERT: K 145 TYR cc_start: 0.7175 (t80) cc_final: 0.6701 (t80) REVERT: L 10 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: L 83 MET cc_start: 0.8354 (tpp) cc_final: 0.8137 (mmt) REVERT: L 181 GLN cc_start: 0.7748 (tt0) cc_final: 0.6818 (mt0) outliers start: 61 outliers final: 44 residues processed: 295 average time/residue: 2.0867 time to fit residues: 701.6715 Evaluate side-chains 300 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 2.975 ------------------------------------------------------------------------------- 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 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 C residue 31 ASP Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain 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 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 12 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN K 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102231 restraints weight = 29897.494| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.53 r_work: 0.2815 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22092 Z= 0.161 Angle : 0.645 16.626 30108 Z= 0.311 Chirality : 0.047 0.322 3507 Planarity : 0.004 0.041 3777 Dihedral : 8.050 59.225 3983 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.70 % Allowed : 15.88 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2670 helix: 2.73 (0.26), residues: 366 sheet: 0.20 (0.18), residues: 837 loop : -0.95 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 50 HIS 0.004 0.001 HIS D 106 PHE 0.015 0.002 PHE D 9 TYR 0.020 0.001 TYR F 162 ARG 0.008 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 18) link_NAG-ASN : angle 2.60905 ( 54) link_ALPHA1-6 : bond 0.00572 ( 9) link_ALPHA1-6 : angle 1.98586 ( 27) link_BETA1-4 : bond 0.00345 ( 15) link_BETA1-4 : angle 1.52266 ( 45) link_ALPHA1-2 : bond 0.00112 ( 3) link_ALPHA1-2 : angle 1.70230 ( 9) link_ALPHA1-3 : bond 0.00635 ( 9) link_ALPHA1-3 : angle 2.88061 ( 27) hydrogen bonds : bond 0.03393 ( 872) hydrogen bonds : angle 4.96596 ( 2319) SS BOND : bond 0.00347 ( 30) SS BOND : angle 2.47383 ( 60) covalent geometry : bond 0.00375 (22008) covalent geometry : angle 0.61569 (29886) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 2.423 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: 0.8401 (m-30) cc_final: 0.8168 (m-30) REVERT: A 104 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7828 (t0) REVERT: A 189 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8700 (tm-30) REVERT: B 17 MET cc_start: 0.8712 (ttm) cc_final: 0.8004 (ttm) REVERT: B 150 GLU cc_start: 0.7893 (pp20) cc_final: 0.7144 (tp30) REVERT: C 35 GLU cc_start: 0.8657 (tt0) cc_final: 0.8303 (tt0) REVERT: C 173 ASN cc_start: 0.8548 (p0) cc_final: 0.8010 (t0) REVERT: D 12 ASN cc_start: 0.7963 (t0) cc_final: 0.7555 (t0) REVERT: D 150 GLU cc_start: 0.7834 (pp20) cc_final: 0.7231 (tp30) REVERT: E 173 ASN cc_start: 0.8438 (p0) cc_final: 0.7702 (t0) REVERT: F 12 ASN cc_start: 0.8073 (t0) cc_final: 0.7625 (t0) REVERT: F 17 MET cc_start: 0.8874 (ttm) cc_final: 0.8640 (ttm) REVERT: F 53 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7206 (p0) REVERT: F 62 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: F 123 ARG cc_start: 0.8939 (ttp-170) cc_final: 0.8588 (ttp80) REVERT: F 133 MET cc_start: 0.9286 (mtm) cc_final: 0.8985 (mtp) REVERT: F 150 GLU cc_start: 0.7977 (pp20) cc_final: 0.7141 (tp30) REVERT: G 16 GLN cc_start: 0.7006 (pm20) cc_final: 0.6717 (pm20) REVERT: G 81 GLN cc_start: 0.8103 (pm20) cc_final: 0.7781 (pm20) REVERT: H 38 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8636 (ptp-170) REVERT: H 65 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8134 (mm-40) REVERT: H 81 MET cc_start: 0.9189 (ttp) cc_final: 0.8910 (ttt) REVERT: H 155 TYR cc_start: 0.6097 (p90) cc_final: 0.5590 (p90) REVERT: H 171 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7275 (p) REVERT: H 179 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8158 (t) REVERT: I 87 ASP cc_start: 0.8156 (t0) cc_final: 0.7897 (t0) REVERT: J 38 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7866 (ptp-170) REVERT: J 90 ASP cc_start: 0.8473 (m-30) cc_final: 0.8217 (m-30) REVERT: J 181 GLN cc_start: 0.7601 (tt0) cc_final: 0.6708 (mt0) REVERT: J 185 LEU cc_start: 0.8369 (mp) cc_final: 0.7757 (mt) REVERT: K 107 LYS cc_start: 0.8444 (mtpm) cc_final: 0.8013 (mtpt) REVERT: K 141 LEU cc_start: 0.6697 (mp) cc_final: 0.5963 (tt) REVERT: K 145 TYR cc_start: 0.7176 (t80) cc_final: 0.6713 (t80) REVERT: L 10 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: L 83 MET cc_start: 0.8377 (tpp) cc_final: 0.8110 (mmt) REVERT: L 181 GLN cc_start: 0.7744 (tt0) cc_final: 0.6807 (mt0) outliers start: 63 outliers final: 46 residues processed: 297 average time/residue: 1.4714 time to fit residues: 495.4535 Evaluate side-chains 306 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 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 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 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 36 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102690 restraints weight = 29827.605| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.48 r_work: 0.2839 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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: 2 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22092 Z= 0.142 Angle : 0.646 14.796 30108 Z= 0.312 Chirality : 0.047 0.356 3507 Planarity : 0.004 0.041 3777 Dihedral : 7.817 57.610 3983 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.40 % Allowed : 16.65 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2670 helix: 2.80 (0.26), residues: 366 sheet: 0.13 (0.18), residues: 855 loop : -0.88 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 174 PHE 0.015 0.001 PHE D 9 TYR 0.022 0.001 TYR F 162 ARG 0.008 0.000 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 18) link_NAG-ASN : angle 2.57815 ( 54) link_ALPHA1-6 : bond 0.00603 ( 9) link_ALPHA1-6 : angle 1.93433 ( 27) link_BETA1-4 : bond 0.00355 ( 15) link_BETA1-4 : angle 1.45207 ( 45) link_ALPHA1-2 : bond 0.00151 ( 3) link_ALPHA1-2 : angle 1.66623 ( 9) link_ALPHA1-3 : bond 0.00683 ( 9) link_ALPHA1-3 : angle 2.83940 ( 27) hydrogen bonds : bond 0.03345 ( 872) hydrogen bonds : angle 4.92050 ( 2319) SS BOND : bond 0.00457 ( 30) SS BOND : angle 2.84475 ( 60) covalent geometry : bond 0.00327 (22008) covalent geometry : angle 0.61391 (29886) *********************** 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 316 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8486 (m-30) cc_final: 0.8263 (m-30) REVERT: A 104 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 189 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8701 (tm-30) REVERT: B 11 GLU cc_start: 0.8112 (pp20) cc_final: 0.7885 (pp20) REVERT: B 17 MET cc_start: 0.8761 (ttm) cc_final: 0.8091 (ttm) REVERT: B 150 GLU cc_start: 0.7885 (pp20) cc_final: 0.7171 (tp30) REVERT: C 35 GLU cc_start: 0.8606 (tt0) cc_final: 0.8270 (tt0) REVERT: C 173 ASN cc_start: 0.8526 (p0) cc_final: 0.8017 (t0) REVERT: C 260 MET cc_start: 0.9240 (mtp) cc_final: 0.9005 (mtp) REVERT: D 12 ASN cc_start: 0.7973 (t0) cc_final: 0.7554 (t0) REVERT: D 150 GLU cc_start: 0.7819 (pp20) cc_final: 0.7241 (tp30) REVERT: E 173 ASN cc_start: 0.8428 (p0) cc_final: 0.7747 (t0) REVERT: F 12 ASN cc_start: 0.8062 (t0) cc_final: 0.7623 (t0) REVERT: F 17 MET cc_start: 0.8723 (ttm) cc_final: 0.8452 (ttm) REVERT: F 53 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7034 (p0) REVERT: F 62 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8362 (mttp) REVERT: F 123 ARG cc_start: 0.8895 (ttp-170) cc_final: 0.8606 (ttp80) REVERT: F 133 MET cc_start: 0.9269 (mtm) cc_final: 0.8967 (mtp) REVERT: F 150 GLU cc_start: 0.7953 (pp20) cc_final: 0.7147 (tp30) REVERT: G 16 GLN cc_start: 0.7047 (pm20) cc_final: 0.6774 (pm20) REVERT: G 68 LYS cc_start: 0.8161 (tttt) cc_final: 0.6313 (tptt) REVERT: H 38 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8622 (ptp-170) REVERT: H 81 MET cc_start: 0.9161 (ttp) cc_final: 0.8878 (ttt) REVERT: H 155 TYR cc_start: 0.6100 (p90) cc_final: 0.5622 (p90) REVERT: H 171 SER cc_start: 0.7667 (OUTLIER) cc_final: 0.7265 (p) REVERT: I 87 ASP cc_start: 0.8166 (t0) cc_final: 0.7885 (t0) REVERT: I 129 GLN cc_start: 0.4736 (tm-30) cc_final: 0.4524 (tt0) REVERT: J 38 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7865 (ptp-170) REVERT: J 90 ASP cc_start: 0.8476 (m-30) cc_final: 0.8214 (m-30) REVERT: J 181 GLN cc_start: 0.7602 (tt0) cc_final: 0.6700 (mt0) REVERT: J 185 LEU cc_start: 0.8386 (mp) cc_final: 0.7769 (mt) REVERT: K 107 LYS cc_start: 0.8435 (mtpm) cc_final: 0.8003 (mtpt) REVERT: K 141 LEU cc_start: 0.6667 (mp) cc_final: 0.5931 (tt) REVERT: K 145 TYR cc_start: 0.7124 (t80) cc_final: 0.6693 (t80) REVERT: L 10 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: L 83 MET cc_start: 0.8340 (tpp) cc_final: 0.8041 (mmt) REVERT: L 181 GLN cc_start: 0.7750 (tt0) cc_final: 0.6819 (mt0) outliers start: 56 outliers final: 45 residues processed: 291 average time/residue: 1.4511 time to fit residues: 480.4854 Evaluate side-chains 307 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 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 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER 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 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 79 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 0.0030 chunk 188 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 177 optimal weight: 10.0000 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103289 restraints weight = 29872.633| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.52 r_work: 0.2847 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22092 Z= 0.128 Angle : 0.642 15.051 30108 Z= 0.310 Chirality : 0.047 0.322 3507 Planarity : 0.004 0.041 3777 Dihedral : 7.547 56.294 3983 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.14 % Allowed : 16.99 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2670 helix: 2.87 (0.26), residues: 366 sheet: 0.20 (0.18), residues: 855 loop : -0.85 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.008 0.001 HIS J 210 PHE 0.016 0.001 PHE B 3 TYR 0.020 0.001 TYR F 162 ARG 0.010 0.000 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 18) link_NAG-ASN : angle 2.56028 ( 54) link_ALPHA1-6 : bond 0.00628 ( 9) link_ALPHA1-6 : angle 1.86844 ( 27) link_BETA1-4 : bond 0.00361 ( 15) link_BETA1-4 : angle 1.37702 ( 45) link_ALPHA1-2 : bond 0.00175 ( 3) link_ALPHA1-2 : angle 1.64416 ( 9) link_ALPHA1-3 : bond 0.00735 ( 9) link_ALPHA1-3 : angle 2.79121 ( 27) hydrogen bonds : bond 0.03276 ( 872) hydrogen bonds : angle 4.86995 ( 2319) SS BOND : bond 0.00307 ( 30) SS BOND : angle 2.78962 ( 60) covalent geometry : bond 0.00294 (22008) covalent geometry : angle 0.61103 (29886) ********************** 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 312 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 2.400 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: 0.8493 (m-30) cc_final: 0.8255 (m-30) REVERT: A 104 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7777 (t0) REVERT: A 189 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8699 (tm-30) REVERT: B 17 MET cc_start: 0.8763 (ttm) cc_final: 0.8106 (ttm) REVERT: B 150 GLU cc_start: 0.7879 (pp20) cc_final: 0.7061 (tp30) REVERT: C 35 GLU cc_start: 0.8618 (tt0) cc_final: 0.8285 (tt0) REVERT: C 173 ASN cc_start: 0.8518 (p0) cc_final: 0.8005 (t0) REVERT: D 12 ASN cc_start: 0.7949 (t0) cc_final: 0.7534 (t0) REVERT: D 150 GLU cc_start: 0.7935 (pp20) cc_final: 0.7321 (tp30) REVERT: E 173 ASN cc_start: 0.8375 (p0) cc_final: 0.7777 (t0) REVERT: F 12 ASN cc_start: 0.8046 (t0) cc_final: 0.7594 (t0) REVERT: F 17 MET cc_start: 0.8739 (ttm) cc_final: 0.8469 (ttm) REVERT: F 53 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7191 (p0) REVERT: F 62 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8356 (mttp) REVERT: F 123 ARG cc_start: 0.8913 (ttp-170) cc_final: 0.8635 (ttp80) REVERT: F 133 MET cc_start: 0.9131 (mtm) cc_final: 0.8838 (mtp) REVERT: F 150 GLU cc_start: 0.7926 (pp20) cc_final: 0.7035 (tp30) REVERT: G 68 LYS cc_start: 0.8207 (tttt) cc_final: 0.6303 (tptt) REVERT: H 81 MET cc_start: 0.9164 (ttp) cc_final: 0.8919 (OUTLIER) REVERT: H 155 TYR cc_start: 0.6089 (p90) cc_final: 0.5788 (p90) REVERT: H 171 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7247 (p) REVERT: I 87 ASP cc_start: 0.8212 (t0) cc_final: 0.7942 (t0) REVERT: I 129 GLN cc_start: 0.4750 (tm-30) cc_final: 0.4523 (tt0) REVERT: J 38 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7898 (ptp-170) REVERT: J 90 ASP cc_start: 0.8470 (m-30) cc_final: 0.8239 (m-30) REVERT: J 181 GLN cc_start: 0.7562 (tt0) cc_final: 0.7137 (mp-120) REVERT: J 185 LEU cc_start: 0.8379 (mp) cc_final: 0.8062 (mt) REVERT: K 107 LYS cc_start: 0.8422 (mtpm) cc_final: 0.7989 (mtpt) REVERT: K 141 LEU cc_start: 0.6645 (mp) cc_final: 0.5916 (tt) REVERT: K 145 TYR cc_start: 0.7181 (t80) cc_final: 0.6814 (t80) REVERT: L 10 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: L 83 MET cc_start: 0.8312 (tpp) cc_final: 0.8025 (mmt) REVERT: L 181 GLN cc_start: 0.7760 (tt0) cc_final: 0.6830 (mt0) outliers start: 50 outliers final: 45 residues processed: 288 average time/residue: 1.4974 time to fit residues: 489.0224 Evaluate side-chains 311 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 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 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103411 restraints weight = 29867.810| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.50 r_work: 0.2805 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.333 22092 Z= 0.218 Angle : 0.838 59.154 30108 Z= 0.444 Chirality : 0.048 0.470 3507 Planarity : 0.004 0.041 3777 Dihedral : 7.550 56.297 3983 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.48 % Allowed : 16.82 % Favored : 80.70 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2670 helix: 2.87 (0.26), residues: 366 sheet: 0.20 (0.18), residues: 855 loop : -0.86 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.009 0.001 HIS J 210 PHE 0.014 0.001 PHE F 9 TYR 0.018 0.001 TYR F 162 ARG 0.008 0.000 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 18) link_NAG-ASN : angle 2.55918 ( 54) link_ALPHA1-6 : bond 0.00626 ( 9) link_ALPHA1-6 : angle 1.86760 ( 27) link_BETA1-4 : bond 0.00366 ( 15) link_BETA1-4 : angle 1.38041 ( 45) link_ALPHA1-2 : bond 0.00181 ( 3) link_ALPHA1-2 : angle 1.64559 ( 9) link_ALPHA1-3 : bond 0.00736 ( 9) link_ALPHA1-3 : angle 2.78907 ( 27) hydrogen bonds : bond 0.03287 ( 872) hydrogen bonds : angle 4.87027 ( 2319) SS BOND : bond 0.01611 ( 30) SS BOND : angle 4.79253 ( 60) covalent geometry : bond 0.00479 (22008) covalent geometry : angle 0.79695 (29886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25120.28 seconds wall clock time: 438 minutes 34.77 seconds (26314.77 seconds total)