Starting phenix.real_space_refine on Sat Jul 4 15:19:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.map" model { file = "/net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k37_22652/07_2026/7k37_22652.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21561 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.97, per 1000 atoms: 0.23 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=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 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=2.11 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 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=1.95 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 881.5 milliseconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4962 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 65 sheets defined 19.1% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.201A 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: 4.462A 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 158 through 161 removed outlier: 3.542A pdb=" N VAL B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 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: 5.201A 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: 4.463A 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 158 through 161 removed outlier: 3.541A pdb=" N VAL D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 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: 5.201A 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: 4.463A 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 158 through 161 removed outlier: 3.541A pdb=" N VAL F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'G' and resid 126 through 132 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.778A 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 195 through 202 removed outlier: 4.516A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.521A 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 195 through 202 removed outlier: 4.517A pdb=" N GLY J 200 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.817A 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 195 through 202 removed outlier: 4.518A pdb=" N GLY L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 14 removed outlier: 8.132A pdb=" N TRP B 14 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 17 " --> pdb=" O TRP B 14 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 8.132A pdb=" N TRP B 14 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 17 " --> pdb=" O TRP B 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.012A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB2, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.725A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.189A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.744A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.012A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.726A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.189A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 13 through 14 removed outlier: 8.175A pdb=" N TRP F 14 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS E 17 " --> pdb=" O TRP F 14 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 13 through 14 removed outlier: 8.175A pdb=" N TRP F 14 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS E 17 " --> pdb=" O TRP F 14 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD2, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD3, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.013A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD6, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD9, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.726A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE2, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.190A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.538A pdb=" N THR G 109 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.557A pdb=" N PHE G 123 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.127A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR G 197 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 130 through 134 removed outlier: 5.918A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 160 through 164 Processing sheet with id=AF3, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.840A pdb=" N THR I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.460A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.743A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER I 179 " --> pdb=" O THR I 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 150 through 154 Processing sheet with id=AF7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 130 through 134 removed outlier: 5.919A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 160 through 164 Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.615A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.736A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER K 136 " --> pdb=" O LEU K 186 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU K 186 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL K 138 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU K 184 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU K 140 " --> pdb=" O SER K 182 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER K 182 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN K 142 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU K 180 " --> pdb=" O ASN K 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 158 through 159 removed outlier: 3.565A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR K 202 " --> pdb=" O LYS K 150 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 130 through 134 removed outlier: 5.919A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 160 through 164 904 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 2.42 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: 6937 1.34 - 1.46: 5361 1.46 - 1.58: 9572 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 22008 Sorted by residual: bond pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 1.408 1.450 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" C3 MAN O 4 " pdb=" O3 MAN O 4 " ideal model delta sigma weight residual 1.408 1.449 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C3 MAN R 4 " pdb=" O3 MAN R 4 " ideal model delta sigma weight residual 1.408 1.449 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C5 MAN O 4 " pdb=" O5 MAN O 4 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C5 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.418 1.457 -0.039 2.00e-02 2.50e+03 3.88e+00 ... (remaining 22003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 28902 1.76 - 3.52: 778 3.52 - 5.28: 148 5.28 - 7.04: 50 7.04 - 8.79: 8 Bond angle restraints: 29886 Sorted by residual: angle pdb=" C GLY K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLY I 52 " pdb=" N ASN I 53 " pdb=" CA ASN I 53 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N GLN G 16 " pdb=" CA GLN G 16 " pdb=" C GLN G 16 " ideal model delta sigma weight residual 108.34 112.74 -4.40 1.31e+00 5.83e-01 1.13e+01 angle pdb=" N LYS G 195 " pdb=" CA LYS G 195 " pdb=" C LYS G 195 " ideal model delta sigma weight residual 110.80 117.37 -6.57 2.13e+00 2.20e-01 9.52e+00 angle pdb=" C2 MAN U 4 " pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 107.58 116.37 -8.79 3.00e+00 1.11e-01 8.59e+00 ... (remaining 29881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 11729 17.85 - 35.69: 862 35.69 - 53.54: 115 53.54 - 71.38: 44 71.38 - 89.23: 15 Dihedral angle restraints: 12765 sinusoidal: 5007 harmonic: 7758 Sorted by residual: 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 3.77 89.23 1 1.00e+01 1.00e-02 9.47e+01 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 28.41 64.59 1 1.00e+01 1.00e-02 5.48e+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 -73.00 2.36 -75.36 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 12762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3106 0.081 - 0.161: 376 0.161 - 0.242: 12 0.242 - 0.322: 10 0.322 - 0.403: 3 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 2.07 0.40 2.00e-01 2.50e+01 4.06e+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 2.07 0.40 2.00e-01 2.50e+01 4.03e+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 2.07 0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 3504 not shown) Planarity restraints: 3795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE J 176 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO J 177 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO J 177 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 177 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 176 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO L 177 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 177 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 177 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 176 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO H 177 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 177 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 177 " 0.033 5.00e-02 4.00e+02 ... (remaining 3792 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 426 2.67 - 3.23: 20104 3.23 - 3.79: 34653 3.79 - 4.34: 48237 4.34 - 4.90: 79448 Nonbonded interactions: 182868 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.114 3.040 nonbonded pdb=" O TYR H 54 " pdb=" O6 MAN O 5 " model vdw 2.170 3.040 nonbonded pdb=" O LYS K 150 " pdb=" OG1 THR K 202 " model vdw 2.186 3.040 nonbonded pdb=" O GLY K 24 " pdb=" OG1 THR K 71 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLU F 120 " pdb=" NH1 ARG F 123 " model vdw 2.196 3.120 ... (remaining 182863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.680 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.006 0.082 22092 Z= 0.254 Angle : 0.770 10.048 30108 Z= 0.382 Chirality : 0.052 0.403 3507 Planarity : 0.005 0.061 3777 Dihedral : 12.856 88.154 7713 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2670 helix: 2.31 (0.25), residues: 363 sheet: -0.06 (0.17), residues: 810 loop : -1.00 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 17 TYR 0.018 0.002 TYR I 145 PHE 0.015 0.002 PHE L 156 TRP 0.027 0.002 TRP A 222 HIS 0.004 0.001 HIS J 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (22008) covalent geometry : angle 0.74202 / 0.38 (29886) SS BOND : bond 0.02090 / 1.25 ( 30) SS BOND : angle 1.17110 / 0.67 ( 60) hydrogen bonds : bond 0.14055 / 9.40 ( 862) hydrogen bonds : angle 7.09889 / 4.90 ( 2283) link_ALPHA1-2 : bond 0.00275 / 0.14 ( 3) link_ALPHA1-2 : angle 1.73647 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00266 / 0.14 ( 9) link_ALPHA1-3 : angle 3.64168 / 1.95 ( 27) link_ALPHA1-6 : bond 0.00266 / 0.16 ( 9) link_ALPHA1-6 : angle 2.60700 / 1.50 ( 27) link_BETA1-4 : bond 0.00280 / 0.18 ( 15) link_BETA1-4 : angle 2.03372 / 1.27 ( 45) link_NAG-ASN : bond 0.00697 / 0.41 ( 18) link_NAG-ASN : angle 3.26902 / 2.12 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 33 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8350 (mm-40) REVERT: A 82 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8601 (mm-30) REVERT: A 189 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 219 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8724 (m) REVERT: A 277 CYS cc_start: 0.6400 (p) cc_final: 0.5989 (p) REVERT: B 27 GLN cc_start: 0.7506 (tt0) cc_final: 0.7043 (tp-100) REVERT: C 219 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8742 (t) REVERT: D 72 GLU cc_start: 0.7989 (pm20) cc_final: 0.7788 (pm20) REVERT: D 139 LYS cc_start: 0.8848 (tttp) cc_final: 0.8629 (tttm) REVERT: E 82 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8532 (mm-30) REVERT: E 189 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7927 (tm-30) REVERT: E 219 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8398 (m) REVERT: F 72 GLU cc_start: 0.8264 (pm20) cc_final: 0.7965 (pm20) REVERT: F 133 MET cc_start: 0.8484 (mtm) cc_final: 0.7924 (mtp) REVERT: G 55 ASN cc_start: 0.7938 (t0) cc_final: 0.7705 (t0) REVERT: G 63 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6853 (mtm110) REVERT: G 174 LYS cc_start: 0.7064 (pttm) cc_final: 0.6387 (mtmm) REVERT: H 82 GLU cc_start: 0.8275 (tt0) cc_final: 0.8061 (tt0) REVERT: H 155 TYR cc_start: 0.7662 (p90) cc_final: 0.7443 (p90) REVERT: I 55 ASN cc_start: 0.8219 (t0) cc_final: 0.7962 (t0) REVERT: I 154 LYS cc_start: 0.6265 (tmtt) cc_final: 0.6029 (tptm) REVERT: J 3 GLN cc_start: 0.8360 (tt0) cc_final: 0.8130 (tt0) REVERT: J 212 PRO cc_start: 0.8648 (Cg_exo) cc_final: 0.8411 (Cg_endo) REVERT: K 63 ARG cc_start: 0.6676 (ptt-90) cc_final: 0.6343 (ptt-90) REVERT: L 87 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7250 (mtt90) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.6712 time to fit residues: 259.7575 Evaluate side-chains 248 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain E residue 219 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN A 211 GLN B 34 GLN B 125 GLN B 168 ASN B 172 GLN D 78 GLN D 125 GLN F 34 GLN F 78 GLN F 172 GLN G 36 HIS H 43 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN K 36 HIS ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.096686 restraints weight = 28299.609| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.05 r_work: 0.2791 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1296 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= 0.190 Angle : 0.691 10.136 30108 Z= 0.336 Chirality : 0.049 0.357 3507 Planarity : 0.005 0.049 3777 Dihedral : 5.027 35.085 2904 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.63 % Allowed : 8.86 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2670 helix: 2.58 (0.25), residues: 366 sheet: -0.20 (0.17), residues: 885 loop : -1.02 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 321 TYR 0.013 0.002 TYR I 197 PHE 0.014 0.002 PHE F 9 TRP 0.015 0.002 TRP L 47 HIS 0.008 0.002 HIS G 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (22008) covalent geometry : angle 0.66647 / 0.33 (29886) SS BOND : bond 0.00470 / 0.30 ( 30) SS BOND : angle 1.12364 / 0.64 ( 60) hydrogen bonds : bond 0.03848 / 2.53 ( 862) hydrogen bonds : angle 5.94370 / 4.12 ( 2283) link_ALPHA1-2 : bond 0.00265 / 0.14 ( 3) link_ALPHA1-2 : angle 1.64213 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00372 / 0.20 ( 9) link_ALPHA1-3 : angle 2.93214 / 1.55 ( 27) link_ALPHA1-6 : bond 0.00364 / 0.23 ( 9) link_ALPHA1-6 : angle 2.12114 / 1.21 ( 27) link_BETA1-4 : bond 0.00298 / 0.19 ( 15) link_BETA1-4 : angle 1.92405 / 1.27 ( 45) link_NAG-ASN : bond 0.00807 / 0.48 ( 18) link_NAG-ASN : angle 2.99724 / 1.94 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8655 (mm-40) REVERT: A 82 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9109 (mm-30) REVERT: A 189 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 211 GLN cc_start: 0.8738 (tt0) cc_final: 0.8512 (tt0) REVERT: B 27 GLN cc_start: 0.8264 (tt0) cc_final: 0.7894 (tp-100) REVERT: B 38 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8591 (mm) REVERT: C 31 ASP cc_start: 0.8715 (m-30) cc_final: 0.8479 (m-30) REVERT: D 72 GLU cc_start: 0.8673 (pm20) cc_final: 0.8305 (pm20) REVERT: D 150 GLU cc_start: 0.8453 (pp20) cc_final: 0.8079 (tm-30) REVERT: E 189 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8310 (tm-30) REVERT: E 219 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8621 (m) REVERT: F 27 GLN cc_start: 0.8082 (tp40) cc_final: 0.7772 (tm-30) REVERT: F 72 GLU cc_start: 0.8821 (pm20) cc_final: 0.8601 (pm20) REVERT: G 87 ASP cc_start: 0.8360 (t0) cc_final: 0.8083 (t0) REVERT: G 154 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5384 (mtmt) REVERT: G 174 LYS cc_start: 0.6786 (pttm) cc_final: 0.6394 (mtmm) REVERT: I 20 ILE cc_start: 0.9079 (mt) cc_final: 0.8753 (mp) REVERT: I 55 ASN cc_start: 0.8717 (t0) cc_final: 0.8494 (t0) REVERT: I 107 LYS cc_start: 0.8418 (tptp) cc_final: 0.8175 (tppt) REVERT: J 212 PRO cc_start: 0.8664 (Cg_exo) cc_final: 0.8354 (Cg_endo) REVERT: K 81 GLN cc_start: 0.7216 (mt0) cc_final: 0.6825 (mp10) outliers start: 38 outliers final: 16 residues processed: 305 average time/residue: 0.6731 time to fit residues: 229.6889 Evaluate side-chains 255 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 231 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 223 optimal weight: 0.0040 chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 252 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 191 GLN C 210 GLN D 34 GLN D 78 GLN D 125 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 43 GLN H 181 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095962 restraints weight = 28488.538| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.23 r_work: 0.2789 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 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 = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22092 Z= 0.188 Angle : 0.663 10.014 30108 Z= 0.323 Chirality : 0.048 0.343 3507 Planarity : 0.005 0.046 3777 Dihedral : 4.841 31.548 2902 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.31 % Allowed : 11.25 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2670 helix: 2.55 (0.25), residues: 366 sheet: -0.14 (0.17), residues: 894 loop : -1.02 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 321 TYR 0.012 0.002 TYR D 162 PHE 0.013 0.002 PHE F 9 TRP 0.014 0.002 TRP H 47 HIS 0.010 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (22008) covalent geometry : angle 0.63684 / 0.32 (29886) SS BOND : bond 0.00622 / 0.36 ( 30) SS BOND : angle 1.67314 / 0.93 ( 60) hydrogen bonds : bond 0.03751 / 2.46 ( 862) hydrogen bonds : angle 5.76219 / 3.99 ( 2283) link_ALPHA1-2 : bond 0.00306 / 0.15 ( 3) link_ALPHA1-2 : angle 1.41682 / 0.79 ( 9) link_ALPHA1-3 : bond 0.00332 / 0.19 ( 9) link_ALPHA1-3 : angle 2.83552 / 1.46 ( 27) link_ALPHA1-6 : bond 0.00356 / 0.22 ( 9) link_ALPHA1-6 : angle 2.02255 / 1.16 ( 27) link_BETA1-4 : bond 0.00306 / 0.20 ( 15) link_BETA1-4 : angle 1.77314 / 1.15 ( 45) link_NAG-ASN : bond 0.00759 / 0.45 ( 18) link_NAG-ASN : angle 2.90897 / 1.88 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9086 (mm-30) REVERT: A 189 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 27 GLN cc_start: 0.8254 (tt0) cc_final: 0.7850 (tp-100) REVERT: B 38 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8598 (mm) REVERT: C 31 ASP cc_start: 0.8685 (m-30) cc_final: 0.8469 (m-30) REVERT: D 11 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8199 (pp20) REVERT: D 72 GLU cc_start: 0.8699 (pm20) cc_final: 0.8316 (pm20) REVERT: D 74 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: D 78 GLN cc_start: 0.9123 (tt0) cc_final: 0.8760 (tt0) REVERT: D 81 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8667 (mt-10) REVERT: D 150 GLU cc_start: 0.8437 (pp20) cc_final: 0.8054 (tm-30) REVERT: E 189 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8233 (tm-30) REVERT: E 321 ARG cc_start: 0.8930 (ttt90) cc_final: 0.8649 (mtp180) REVERT: F 27 GLN cc_start: 0.8105 (tp40) cc_final: 0.7788 (tm-30) REVERT: F 72 GLU cc_start: 0.8779 (pm20) cc_final: 0.8549 (pm20) REVERT: G 87 ASP cc_start: 0.8325 (t0) cc_final: 0.8032 (t70) REVERT: G 174 LYS cc_start: 0.6857 (pttm) cc_final: 0.6448 (mtmm) REVERT: H 82 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: H 181 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7248 (mt0) REVERT: I 20 ILE cc_start: 0.9067 (mt) cc_final: 0.8774 (mp) REVERT: I 55 ASN cc_start: 0.8708 (t0) cc_final: 0.8461 (t0) REVERT: I 107 LYS cc_start: 0.8339 (tptp) cc_final: 0.8138 (tptt) REVERT: J 82 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: J 212 PRO cc_start: 0.8565 (Cg_exo) cc_final: 0.8301 (Cg_endo) REVERT: K 81 GLN cc_start: 0.7291 (mt0) cc_final: 0.6832 (mp10) REVERT: K 165 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6989 (mm-40) REVERT: L 62 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8661 (mmtt) outliers start: 54 outliers final: 27 residues processed: 279 average time/residue: 0.6208 time to fit residues: 195.5524 Evaluate side-chains 265 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 54 TYR 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 181 GLN Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 115 optimal weight: 2.9990 chunk 221 optimal weight: 0.0870 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 172 GLN D 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 36 HIS ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096272 restraints weight = 28446.153| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.18 r_work: 0.2802 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22092 Z= 0.177 Angle : 0.663 12.422 30108 Z= 0.322 Chirality : 0.048 0.370 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.734 20.244 2901 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.40 % Allowed : 13.05 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2670 helix: 2.56 (0.26), residues: 366 sheet: -0.10 (0.17), residues: 891 loop : -1.00 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 321 TYR 0.014 0.001 TYR D 162 PHE 0.012 0.002 PHE F 9 TRP 0.013 0.001 TRP H 47 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (22008) covalent geometry : angle 0.63142 / 0.31 (29886) SS BOND : bond 0.00676 / 0.41 ( 30) SS BOND : angle 2.55366 / 1.46 ( 60) hydrogen bonds : bond 0.03564 / 2.34 ( 862) hydrogen bonds : angle 5.63243 / 3.90 ( 2283) link_ALPHA1-2 : bond 0.00326 / 0.16 ( 3) link_ALPHA1-2 : angle 1.38930 / 0.78 ( 9) link_ALPHA1-3 : bond 0.00329 / 0.19 ( 9) link_ALPHA1-3 : angle 2.78875 / 1.44 ( 27) link_ALPHA1-6 : bond 0.00356 / 0.22 ( 9) link_ALPHA1-6 : angle 2.03526 / 1.16 ( 27) link_BETA1-4 : bond 0.00271 / 0.18 ( 15) link_BETA1-4 : angle 1.71866 / 1.11 ( 45) link_NAG-ASN : bond 0.00668 / 0.40 ( 18) link_NAG-ASN : angle 2.91180 / 1.90 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9317 (mm-30) cc_final: 0.9069 (mm-30) REVERT: A 189 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 27 GLN cc_start: 0.8264 (tt0) cc_final: 0.7885 (tp-100) REVERT: B 38 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8590 (mm) REVERT: C 31 ASP cc_start: 0.8651 (m-30) cc_final: 0.8405 (m-30) REVERT: D 72 GLU cc_start: 0.8722 (pm20) cc_final: 0.8301 (pm20) REVERT: D 150 GLU cc_start: 0.8444 (pp20) cc_final: 0.8069 (tm-30) REVERT: E 189 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8266 (tm-30) REVERT: E 190 GLU cc_start: 0.8811 (tt0) cc_final: 0.8598 (pt0) REVERT: E 219 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8677 (m) REVERT: F 27 GLN cc_start: 0.8106 (tp40) cc_final: 0.7802 (tm-30) REVERT: F 74 GLU cc_start: 0.8289 (mp0) cc_final: 0.7966 (mp0) REVERT: G 87 ASP cc_start: 0.8282 (t0) cc_final: 0.7984 (t0) REVERT: G 174 LYS cc_start: 0.6839 (pttm) cc_final: 0.6419 (mtmm) REVERT: I 20 ILE cc_start: 0.9073 (mt) cc_final: 0.8807 (mp) REVERT: I 55 ASN cc_start: 0.8686 (t0) cc_final: 0.8450 (t0) REVERT: J 82 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: J 212 PRO cc_start: 0.8625 (Cg_exo) cc_final: 0.8362 (Cg_endo) REVERT: K 63 ARG cc_start: 0.7432 (ptt-90) cc_final: 0.6869 (ptt90) REVERT: K 81 GLN cc_start: 0.7220 (mt0) cc_final: 0.6854 (mp10) REVERT: K 165 GLN cc_start: 0.7276 (mm-40) cc_final: 0.7023 (mm-40) REVERT: L 62 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8767 (mmtt) outliers start: 56 outliers final: 27 residues processed: 291 average time/residue: 0.6440 time to fit residues: 210.8654 Evaluate side-chains 259 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL 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 I residue 36 HIS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 14 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 236 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 172 GLN D 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 36 HIS G 143 ASN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096859 restraints weight = 28274.257| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.27 r_work: 0.2811 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22092 Z= 0.171 Angle : 0.674 17.391 30108 Z= 0.327 Chirality : 0.048 0.346 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.724 27.011 2901 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.44 % Allowed : 14.04 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2670 helix: 2.57 (0.26), residues: 366 sheet: -0.03 (0.17), residues: 885 loop : -0.99 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.012 0.001 TYR D 162 PHE 0.014 0.002 PHE F 9 TRP 0.013 0.001 TRP H 47 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (22008) covalent geometry : angle 0.64139 / 0.32 (29886) SS BOND : bond 0.00540 / 0.34 ( 30) SS BOND : angle 2.84734 / 1.63 ( 60) hydrogen bonds : bond 0.03486 / 2.28 ( 862) hydrogen bonds : angle 5.53146 / 3.82 ( 2283) link_ALPHA1-2 : bond 0.00330 / 0.17 ( 3) link_ALPHA1-2 : angle 1.38733 / 0.78 ( 9) link_ALPHA1-3 : bond 0.00332 / 0.19 ( 9) link_ALPHA1-3 : angle 2.76341 / 1.43 ( 27) link_ALPHA1-6 : bond 0.00344 / 0.21 ( 9) link_ALPHA1-6 : angle 2.03602 / 1.16 ( 27) link_BETA1-4 : bond 0.00287 / 0.19 ( 15) link_BETA1-4 : angle 1.67687 / 1.08 ( 45) link_NAG-ASN : bond 0.00699 / 0.41 ( 18) link_NAG-ASN : angle 2.84814 / 1.85 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9074 (mm-30) REVERT: A 189 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 27 GLN cc_start: 0.8316 (tt0) cc_final: 0.7982 (tp-100) REVERT: B 38 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8601 (mm) REVERT: C 31 ASP cc_start: 0.8666 (m-30) cc_final: 0.8419 (m-30) REVERT: C 195 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: C 209 SER cc_start: 0.9217 (p) cc_final: 0.8885 (m) REVERT: D 11 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8283 (pp20) REVERT: D 72 GLU cc_start: 0.8755 (pm20) cc_final: 0.8333 (pm20) REVERT: D 150 GLU cc_start: 0.8455 (pp20) cc_final: 0.8084 (tm-30) REVERT: E 189 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8278 (tm-30) REVERT: F 27 GLN cc_start: 0.8099 (tp40) cc_final: 0.7712 (tm-30) REVERT: G 87 ASP cc_start: 0.8249 (t0) cc_final: 0.7930 (t0) REVERT: G 174 LYS cc_start: 0.6837 (pttm) cc_final: 0.6427 (mtmm) REVERT: I 20 ILE cc_start: 0.9055 (mt) cc_final: 0.8788 (mp) REVERT: I 55 ASN cc_start: 0.8532 (t0) cc_final: 0.8312 (t0) REVERT: J 82 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: J 212 PRO cc_start: 0.8608 (Cg_exo) cc_final: 0.8348 (Cg_endo) REVERT: K 63 ARG cc_start: 0.7442 (ptt-90) cc_final: 0.7225 (ptt90) REVERT: K 81 GLN cc_start: 0.7296 (mt0) cc_final: 0.6970 (mm-40) REVERT: K 165 GLN cc_start: 0.7254 (mm-40) cc_final: 0.7015 (mm-40) REVERT: L 62 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8773 (mmtt) outliers start: 57 outliers final: 31 residues processed: 277 average time/residue: 0.6633 time to fit residues: 206.7165 Evaluate side-chains 268 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 138 VAL 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 I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 181 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 172 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 105 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 43 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094527 restraints weight = 28349.184| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.22 r_work: 0.2772 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 22092 Z= 0.293 Angle : 0.741 16.893 30108 Z= 0.362 Chirality : 0.051 0.381 3507 Planarity : 0.005 0.051 3777 Dihedral : 4.901 26.018 2901 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.87 % Allowed : 14.46 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2670 helix: 2.01 (0.26), residues: 384 sheet: -0.14 (0.17), residues: 888 loop : -1.03 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.015 0.002 TYR E 195 PHE 0.017 0.002 PHE F 9 TRP 0.015 0.002 TRP H 47 HIS 0.014 0.002 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.29 (22008) covalent geometry : angle 0.70986 / 0.35 (29886) SS BOND : bond 0.00728 / 0.47 ( 30) SS BOND : angle 2.73598 / 1.58 ( 60) hydrogen bonds : bond 0.03961 / 2.59 ( 862) hydrogen bonds : angle 5.66584 / 3.92 ( 2283) link_ALPHA1-2 : bond 0.00218 / 0.11 ( 3) link_ALPHA1-2 : angle 1.44636 / 0.81 ( 9) link_ALPHA1-3 : bond 0.00392 / 0.22 ( 9) link_ALPHA1-3 : angle 2.88554 / 1.50 ( 27) link_ALPHA1-6 : bond 0.00395 / 0.26 ( 9) link_ALPHA1-6 : angle 2.03731 / 1.18 ( 27) link_BETA1-4 : bond 0.00415 / 0.27 ( 15) link_BETA1-4 : angle 1.97872 / 1.27 ( 45) link_NAG-ASN : bond 0.00816 / 0.51 ( 18) link_NAG-ASN : angle 3.04684 / 1.96 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9103 (mm-30) REVERT: A 189 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 27 GLN cc_start: 0.8310 (tt0) cc_final: 0.7978 (tp-100) REVERT: B 38 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8610 (mm) REVERT: C 31 ASP cc_start: 0.8678 (m-30) cc_final: 0.8432 (m-30) REVERT: C 195 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: C 209 SER cc_start: 0.9146 (p) cc_final: 0.8895 (m) REVERT: D 72 GLU cc_start: 0.8786 (pm20) cc_final: 0.8347 (pm20) REVERT: D 81 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: D 150 GLU cc_start: 0.8468 (pp20) cc_final: 0.8026 (tm-30) REVERT: E 189 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8127 (tm-30) REVERT: E 190 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: F 27 GLN cc_start: 0.8189 (tp40) cc_final: 0.7887 (tm-30) REVERT: G 87 ASP cc_start: 0.8339 (t0) cc_final: 0.8009 (t0) REVERT: G 174 LYS cc_start: 0.7007 (pttm) cc_final: 0.6306 (mtmm) REVERT: G 184 LEU cc_start: 0.7325 (pt) cc_final: 0.6997 (tp) REVERT: H 82 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: H 186 TYR cc_start: 0.7291 (m-80) cc_final: 0.7068 (m-80) REVERT: I 20 ILE cc_start: 0.9081 (mt) cc_final: 0.8835 (mp) REVERT: I 55 ASN cc_start: 0.8734 (t0) cc_final: 0.8483 (t0) REVERT: J 82 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: J 212 PRO cc_start: 0.8620 (Cg_exo) cc_final: 0.8368 (Cg_endo) REVERT: K 63 ARG cc_start: 0.7493 (ptt-90) cc_final: 0.7229 (ptt-90) REVERT: K 81 GLN cc_start: 0.7314 (mt0) cc_final: 0.7055 (mm-40) REVERT: L 62 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8784 (mmtt) outliers start: 67 outliers final: 34 residues processed: 279 average time/residue: 0.6089 time to fit residues: 191.4297 Evaluate side-chains 268 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 128 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 chunk 200 optimal weight: 8.9990 chunk 31 optimal weight: 0.1980 chunk 191 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 60 ASN B 172 GLN D 34 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN K 6 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097607 restraints weight = 28061.656| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.90 r_work: 0.2825 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22092 Z= 0.128 Angle : 0.645 13.338 30108 Z= 0.314 Chirality : 0.047 0.364 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.639 24.917 2901 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.48 % Allowed : 15.15 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2670 helix: 2.56 (0.26), residues: 366 sheet: -0.15 (0.17), residues: 918 loop : -0.90 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 321 TYR 0.015 0.001 TYR D 162 PHE 0.016 0.001 PHE B 24 TRP 0.015 0.001 TRP L 47 HIS 0.008 0.001 HIS I 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (22008) covalent geometry : angle 0.61655 / 0.31 (29886) SS BOND : bond 0.00741 / 0.46 ( 30) SS BOND : angle 2.24065 / 1.28 ( 60) hydrogen bonds : bond 0.03297 / 2.16 ( 862) hydrogen bonds : angle 5.41831 / 3.74 ( 2283) link_ALPHA1-2 : bond 0.00418 / 0.21 ( 3) link_ALPHA1-2 : angle 1.32495 / 0.74 ( 9) link_ALPHA1-3 : bond 0.00330 / 0.19 ( 9) link_ALPHA1-3 : angle 2.73299 / 1.42 ( 27) link_ALPHA1-6 : bond 0.00366 / 0.21 ( 9) link_ALPHA1-6 : angle 2.02471 / 1.15 ( 27) link_BETA1-4 : bond 0.00257 / 0.18 ( 15) link_BETA1-4 : angle 1.50784 / 0.97 ( 45) link_NAG-ASN : bond 0.00661 / 0.37 ( 18) link_NAG-ASN : angle 2.79318 / 1.81 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.828 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 70 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.8815 (tp) REVERT: A 189 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 27 GLN cc_start: 0.8246 (tt0) cc_final: 0.7969 (tp-100) REVERT: C 31 ASP cc_start: 0.8629 (m-30) cc_final: 0.8374 (m-30) REVERT: C 195 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: C 209 SER cc_start: 0.9151 (p) cc_final: 0.8894 (m) REVERT: D 72 GLU cc_start: 0.8751 (pm20) cc_final: 0.8297 (pm20) REVERT: D 150 GLU cc_start: 0.8416 (pp20) cc_final: 0.8098 (tm-30) REVERT: E 189 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 190 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8615 (pt0) REVERT: F 27 GLN cc_start: 0.8099 (tp40) cc_final: 0.7748 (tm-30) REVERT: F 133 MET cc_start: 0.8806 (mtm) cc_final: 0.8578 (mtm) REVERT: G 87 ASP cc_start: 0.8198 (t0) cc_final: 0.7853 (t70) REVERT: G 174 LYS cc_start: 0.6648 (pttm) cc_final: 0.6252 (mtmm) REVERT: G 184 LEU cc_start: 0.7145 (pt) cc_final: 0.6900 (tp) REVERT: H 181 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: I 20 ILE cc_start: 0.9033 (mt) cc_final: 0.8778 (mp) REVERT: J 55 ASP cc_start: 0.8545 (p0) cc_final: 0.8333 (p0) REVERT: K 81 GLN cc_start: 0.7280 (mt0) cc_final: 0.6965 (mm-40) REVERT: L 62 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8762 (tmtt) outliers start: 58 outliers final: 28 residues processed: 285 average time/residue: 0.6322 time to fit residues: 203.5245 Evaluate side-chains 267 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL 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 181 GLN Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 54 optimal weight: 0.0670 chunk 97 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 146 optimal weight: 0.0070 chunk 226 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 245 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 172 GLN D 34 GLN D 168 ASN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 43 GLN H 65 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN K 6 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 181 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098737 restraints weight = 29222.324| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.12 r_work: 0.2793 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22092 Z= 0.214 Angle : 0.693 13.435 30108 Z= 0.336 Chirality : 0.049 0.343 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.725 27.134 2901 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.48 % Allowed : 15.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2670 helix: 2.54 (0.26), residues: 366 sheet: -0.18 (0.17), residues: 918 loop : -0.93 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.014 0.002 TYR E 195 PHE 0.016 0.002 PHE F 9 TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (22008) covalent geometry : angle 0.66420 / 0.33 (29886) SS BOND : bond 0.00680 / 0.45 ( 30) SS BOND : angle 2.39773 / 1.38 ( 60) hydrogen bonds : bond 0.03617 / 2.37 ( 862) hydrogen bonds : angle 5.46290 / 3.78 ( 2283) link_ALPHA1-2 : bond 0.00293 / 0.15 ( 3) link_ALPHA1-2 : angle 1.40943 / 0.79 ( 9) link_ALPHA1-3 : bond 0.00355 / 0.20 ( 9) link_ALPHA1-3 : angle 2.76681 / 1.44 ( 27) link_ALPHA1-6 : bond 0.00357 / 0.22 ( 9) link_ALPHA1-6 : angle 2.03856 / 1.17 ( 27) link_BETA1-4 : bond 0.00322 / 0.21 ( 15) link_BETA1-4 : angle 1.74959 / 1.13 ( 45) link_NAG-ASN : bond 0.00719 / 0.44 ( 18) link_NAG-ASN : angle 2.90401 / 1.88 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.785 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 70 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.8848 (tp) REVERT: A 189 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 11 GLU cc_start: 0.8515 (pp20) cc_final: 0.8215 (tm-30) REVERT: B 27 GLN cc_start: 0.8262 (tt0) cc_final: 0.7911 (tp-100) REVERT: C 31 ASP cc_start: 0.8700 (m-30) cc_final: 0.8447 (m-30) REVERT: C 195 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: C 209 SER cc_start: 0.9182 (p) cc_final: 0.8902 (m) REVERT: D 72 GLU cc_start: 0.8759 (pm20) cc_final: 0.8235 (pm20) REVERT: D 150 GLU cc_start: 0.8375 (pp20) cc_final: 0.8024 (tm-30) REVERT: E 189 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 190 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8590 (pt0) REVERT: F 27 GLN cc_start: 0.8189 (tp40) cc_final: 0.7822 (tm-30) REVERT: F 133 MET cc_start: 0.8871 (mtm) cc_final: 0.8587 (mtm) REVERT: G 87 ASP cc_start: 0.8268 (t0) cc_final: 0.7930 (t0) REVERT: G 174 LYS cc_start: 0.6703 (pttm) cc_final: 0.6283 (mtmm) REVERT: G 184 LEU cc_start: 0.7241 (pt) cc_final: 0.7001 (tp) REVERT: I 20 ILE cc_start: 0.9046 (mt) cc_final: 0.8824 (mp) REVERT: K 63 ARG cc_start: 0.6886 (ptt90) cc_final: 0.6491 (ptt-90) REVERT: K 81 GLN cc_start: 0.7323 (mt0) cc_final: 0.6987 (mm-40) REVERT: L 62 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8770 (tmtt) outliers start: 58 outliers final: 36 residues processed: 271 average time/residue: 0.6587 time to fit residues: 201.3218 Evaluate side-chains 264 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 40 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 176 optimal weight: 0.0370 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 60 ASN B 172 GLN D 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.091742 restraints weight = 29175.107| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.31 r_work: 0.2823 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22092 Z= 0.139 Angle : 0.658 14.912 30108 Z= 0.319 Chirality : 0.047 0.342 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.616 29.920 2901 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.35 % Allowed : 15.88 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2670 helix: 2.60 (0.26), residues: 366 sheet: -0.11 (0.17), residues: 918 loop : -0.90 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 321 TYR 0.016 0.001 TYR D 162 PHE 0.016 0.001 PHE D 9 TRP 0.015 0.001 TRP H 50 HIS 0.012 0.001 HIS I 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (22008) covalent geometry : angle 0.62954 / 0.31 (29886) SS BOND : bond 0.00516 / 0.33 ( 30) SS BOND : angle 2.31526 / 1.35 ( 60) hydrogen bonds : bond 0.03321 / 2.17 ( 862) hydrogen bonds : angle 5.34952 / 3.69 ( 2283) link_ALPHA1-2 : bond 0.00381 / 0.19 ( 3) link_ALPHA1-2 : angle 1.35588 / 0.76 ( 9) link_ALPHA1-3 : bond 0.00323 / 0.18 ( 9) link_ALPHA1-3 : angle 2.70350 / 1.40 ( 27) link_ALPHA1-6 : bond 0.00367 / 0.22 ( 9) link_ALPHA1-6 : angle 2.01810 / 1.15 ( 27) link_BETA1-4 : bond 0.00262 / 0.18 ( 15) link_BETA1-4 : angle 1.54247 / 0.99 ( 45) link_NAG-ASN : bond 0.00630 / 0.36 ( 18) link_NAG-ASN : angle 2.79873 / 1.83 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.776 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 70 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.8816 (tp) REVERT: A 89 GLU cc_start: 0.8810 (tt0) cc_final: 0.8540 (mt-10) REVERT: A 189 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 11 GLU cc_start: 0.8502 (pp20) cc_final: 0.8223 (tm-30) REVERT: B 27 GLN cc_start: 0.8220 (tt0) cc_final: 0.7879 (tp-100) REVERT: B 38 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8574 (mm) REVERT: C 31 ASP cc_start: 0.8636 (m-30) cc_final: 0.8378 (m-30) REVERT: C 195 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: C 209 SER cc_start: 0.9167 (p) cc_final: 0.8871 (m) REVERT: D 72 GLU cc_start: 0.8724 (pm20) cc_final: 0.8138 (pm20) REVERT: D 150 GLU cc_start: 0.8303 (pp20) cc_final: 0.7946 (tm-30) REVERT: E 189 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 190 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8454 (pt0) REVERT: F 27 GLN cc_start: 0.8130 (tp40) cc_final: 0.7785 (tm-30) REVERT: F 133 MET cc_start: 0.8697 (mtm) cc_final: 0.8458 (mtm) REVERT: G 87 ASP cc_start: 0.8154 (t0) cc_final: 0.7793 (t0) REVERT: G 174 LYS cc_start: 0.6537 (pttm) cc_final: 0.6157 (mtmm) REVERT: G 184 LEU cc_start: 0.7214 (pt) cc_final: 0.6979 (tp) REVERT: I 20 ILE cc_start: 0.8997 (mt) cc_final: 0.8760 (mp) REVERT: K 81 GLN cc_start: 0.7182 (mt0) cc_final: 0.6850 (mm-40) REVERT: L 62 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8763 (tmtt) outliers start: 55 outliers final: 35 residues processed: 273 average time/residue: 0.5891 time to fit residues: 182.7539 Evaluate side-chains 264 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 205 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 60 ASN B 172 GLN D 34 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 43 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.091823 restraints weight = 29232.704| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.27 r_work: 0.2813 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22092 Z= 0.139 Angle : 0.659 13.929 30108 Z= 0.319 Chirality : 0.047 0.343 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.590 28.841 2901 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.14 % Allowed : 16.05 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2670 helix: 2.65 (0.26), residues: 366 sheet: -0.10 (0.17), residues: 918 loop : -0.90 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 321 TYR 0.015 0.001 TYR D 162 PHE 0.017 0.001 PHE B 24 TRP 0.014 0.001 TRP H 50 HIS 0.006 0.001 HIS I 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (22008) covalent geometry : angle 0.63039 / 0.31 (29886) SS BOND : bond 0.00451 / 0.30 ( 30) SS BOND : angle 2.42579 / 1.41 ( 60) hydrogen bonds : bond 0.03304 / 2.17 ( 862) hydrogen bonds : angle 5.29404 / 3.65 ( 2283) link_ALPHA1-2 : bond 0.00367 / 0.18 ( 3) link_ALPHA1-2 : angle 1.38017 / 0.77 ( 9) link_ALPHA1-3 : bond 0.00316 / 0.18 ( 9) link_ALPHA1-3 : angle 2.67609 / 1.39 ( 27) link_ALPHA1-6 : bond 0.00371 / 0.22 ( 9) link_ALPHA1-6 : angle 2.02038 / 1.15 ( 27) link_BETA1-4 : bond 0.00266 / 0.18 ( 15) link_BETA1-4 : angle 1.53342 / 0.99 ( 45) link_NAG-ASN : bond 0.00640 / 0.37 ( 18) link_NAG-ASN : angle 2.76882 / 1.81 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.796 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 70 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.8811 (tp) REVERT: A 89 GLU cc_start: 0.8826 (tt0) cc_final: 0.8463 (mt-10) REVERT: A 123 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8396 (mt-10) REVERT: A 189 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 190 GLU cc_start: 0.8733 (tt0) cc_final: 0.8525 (tt0) REVERT: B 11 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: B 27 GLN cc_start: 0.8214 (tt0) cc_final: 0.7873 (tp-100) REVERT: C 31 ASP cc_start: 0.8704 (m-30) cc_final: 0.8460 (m-30) REVERT: C 195 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: C 209 SER cc_start: 0.9169 (p) cc_final: 0.8875 (m) REVERT: D 72 GLU cc_start: 0.8686 (pm20) cc_final: 0.8102 (pm20) REVERT: D 150 GLU cc_start: 0.8287 (pp20) cc_final: 0.7934 (tm-30) REVERT: E 189 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8079 (tm-30) REVERT: E 190 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8550 (pt0) REVERT: F 27 GLN cc_start: 0.8112 (tp40) cc_final: 0.7764 (tm-30) REVERT: F 133 MET cc_start: 0.8683 (mtm) cc_final: 0.8461 (mtm) REVERT: G 87 ASP cc_start: 0.8160 (t0) cc_final: 0.7801 (t70) REVERT: G 154 LYS cc_start: 0.6228 (mtpp) cc_final: 0.5728 (mttt) REVERT: G 184 LEU cc_start: 0.7197 (pt) cc_final: 0.6896 (tp) REVERT: H 55 ASP cc_start: 0.8449 (p0) cc_final: 0.8226 (p0) REVERT: I 20 ILE cc_start: 0.8985 (mt) cc_final: 0.8740 (mp) REVERT: K 81 GLN cc_start: 0.7174 (mt0) cc_final: 0.6845 (mm-40) REVERT: L 62 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8765 (tmtt) outliers start: 50 outliers final: 35 residues processed: 265 average time/residue: 0.5865 time to fit residues: 176.3542 Evaluate side-chains 264 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 160 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 172 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096707 restraints weight = 29257.765| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.29 r_work: 0.2795 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22092 Z= 0.210 Angle : 0.695 14.593 30108 Z= 0.337 Chirality : 0.048 0.344 3507 Planarity : 0.004 0.046 3777 Dihedral : 4.698 26.975 2901 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.18 % Allowed : 16.22 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2670 helix: 2.55 (0.26), residues: 366 sheet: -0.15 (0.17), residues: 918 loop : -0.93 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 321 TYR 0.015 0.002 TYR D 162 PHE 0.026 0.002 PHE G 144 TRP 0.013 0.002 TRP H 47 HIS 0.012 0.001 HIS I 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (22008) covalent geometry : angle 0.66607 / 0.33 (29886) SS BOND : bond 0.00557 / 0.37 ( 30) SS BOND : angle 2.56155 / 1.49 ( 60) hydrogen bonds : bond 0.03578 / 2.35 ( 862) hydrogen bonds : angle 5.35914 / 3.70 ( 2283) link_ALPHA1-2 : bond 0.00289 / 0.15 ( 3) link_ALPHA1-2 : angle 1.42245 / 0.80 ( 9) link_ALPHA1-3 : bond 0.00347 / 0.20 ( 9) link_ALPHA1-3 : angle 2.72489 / 1.42 ( 27) link_ALPHA1-6 : bond 0.00359 / 0.22 ( 9) link_ALPHA1-6 : angle 2.02662 / 1.17 ( 27) link_BETA1-4 : bond 0.00308 / 0.20 ( 15) link_BETA1-4 : angle 1.73140 / 1.11 ( 45) link_NAG-ASN : bond 0.00709 / 0.43 ( 18) link_NAG-ASN : angle 2.86909 / 1.87 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9245.77 seconds wall clock time: 158 minutes 15.01 seconds (9495.01 seconds total)