Starting phenix.real_space_refine on Fri Sep 19 00:52:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k37_22652/09_2025/7k37_22652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k37_22652/09_2025/7k37_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k37_22652/09_2025/7k37_22652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k37_22652/09_2025/7k37_22652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k37_22652/09_2025/7k37_22652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k37_22652/09_2025/7k37_22652.map" } 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21561 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.24, per 1000 atoms: 0.29 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: 3.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.25 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: 4.67 Time building geometry restraints manager: 2.61 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 - 22.05: 12989 22.05 - 44.09: 672 44.09 - 66.14: 107 66.14 - 88.18: 52 88.18 - 110.23: 25 Dihedral angle restraints: 13845 sinusoidal: 6087 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 13842 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.660 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 14.710 110.230 8793 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 aren 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 covalent geometry : bond 0.00554 (22008) covalent geometry : angle 0.74202 (29886) SS BOND : bond 0.02090 ( 30) SS BOND : angle 1.17110 ( 60) hydrogen bonds : bond 0.14055 ( 862) hydrogen bonds : angle 7.09889 ( 2283) link_ALPHA1-2 : bond 0.00275 ( 3) link_ALPHA1-2 : angle 1.73647 ( 9) link_ALPHA1-3 : bond 0.00266 ( 9) link_ALPHA1-3 : angle 3.64168 ( 27) link_ALPHA1-6 : bond 0.00266 ( 9) link_ALPHA1-6 : angle 2.60700 ( 27) link_BETA1-4 : bond 0.00280 ( 15) link_BETA1-4 : angle 2.03372 ( 45) link_NAG-ASN : bond 0.00697 ( 18) link_NAG-ASN : angle 3.26902 ( 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 : 0.860 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: 0.8628 (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: 0.7178 (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: 0.7247 time to fit residues: 279.3784 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 : 0.819 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3711 r_free = 0.3711 target = 0.142347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096550 restraints weight = 28292.897| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.38 r_work: 0.2788 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22092 Z= 0.191 Angle : 0.698 9.978 30108 Z= 0.337 Chirality : 0.050 0.349 3507 Planarity : 0.005 0.050 3777 Dihedral : 10.535 80.584 3984 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.58 % Allowed : 8.69 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2670 helix: 2.58 (0.25), residues: 366 sheet: -0.21 (0.17), residues: 885 loop : -1.01 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.006 0.001 HIS G 194 Details of bonding type rmsd covalent geometry : bond 0.00437 (22008) covalent geometry : angle 0.66763 (29886) SS BOND : bond 0.00699 ( 30) SS BOND : angle 1.06411 ( 60) hydrogen bonds : bond 0.03948 ( 862) hydrogen bonds : angle 5.96487 ( 2283) link_ALPHA1-2 : bond 0.00208 ( 3) link_ALPHA1-2 : angle 1.74010 ( 9) link_ALPHA1-3 : bond 0.00581 ( 9) link_ALPHA1-3 : angle 3.55961 ( 27) link_ALPHA1-6 : bond 0.00422 ( 9) link_ALPHA1-6 : angle 2.65513 ( 27) link_BETA1-4 : bond 0.00358 ( 15) link_BETA1-4 : angle 2.23737 ( 45) link_NAG-ASN : bond 0.00879 ( 18) link_NAG-ASN : angle 2.99014 ( 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 322 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8648 (mm-40) REVERT: A 82 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9093 (mm-30) REVERT: A 189 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 211 GLN cc_start: 0.8735 (tt0) cc_final: 0.8511 (tt0) REVERT: B 27 GLN cc_start: 0.8247 (tt0) cc_final: 0.7872 (tp-100) REVERT: B 38 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8584 (mm) REVERT: C 31 ASP cc_start: 0.8770 (m-30) cc_final: 0.8515 (m-30) REVERT: D 72 GLU cc_start: 0.8657 (pm20) cc_final: 0.8292 (pm20) REVERT: E 189 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8295 (tm-30) REVERT: E 219 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8610 (m) REVERT: F 27 GLN cc_start: 0.8072 (tp40) cc_final: 0.7754 (tm-30) REVERT: F 72 GLU cc_start: 0.8797 (pm20) cc_final: 0.8585 (pm20) REVERT: G 154 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5362 (mtmt) REVERT: G 174 LYS cc_start: 0.6846 (pttm) cc_final: 0.6405 (mtmm) REVERT: I 20 ILE cc_start: 0.9077 (mt) cc_final: 0.8745 (mp) REVERT: I 55 ASN cc_start: 0.8724 (t0) cc_final: 0.8503 (t0) REVERT: I 107 LYS cc_start: 0.8383 (tptp) cc_final: 0.8140 (tppt) REVERT: J 212 PRO cc_start: 0.8643 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: K 63 ARG cc_start: 0.7325 (ptt-90) cc_final: 0.7007 (ptt-90) REVERT: K 81 GLN cc_start: 0.7188 (mt0) cc_final: 0.6772 (mp10) outliers start: 37 outliers final: 16 residues processed: 302 average time/residue: 0.7468 time to fit residues: 251.3508 Evaluate side-chains 260 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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: 0.0870 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 223 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 chunk 245 optimal weight: 0.0870 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096822 restraints weight = 28452.513| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.29 r_work: 0.2809 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22092 Z= 0.161 Angle : 0.656 9.840 30108 Z= 0.317 Chirality : 0.048 0.335 3507 Planarity : 0.004 0.045 3777 Dihedral : 10.066 75.565 3982 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.31 % Allowed : 10.91 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2670 helix: 2.59 (0.25), residues: 366 sheet: -0.12 (0.17), residues: 891 loop : -1.01 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 63 TYR 0.012 0.002 TYR D 162 PHE 0.013 0.001 PHE F 9 TRP 0.013 0.001 TRP L 47 HIS 0.013 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00365 (22008) covalent geometry : angle 0.62573 (29886) SS BOND : bond 0.00499 ( 30) SS BOND : angle 1.65218 ( 60) hydrogen bonds : bond 0.03635 ( 862) hydrogen bonds : angle 5.72891 ( 2283) link_ALPHA1-2 : bond 0.00305 ( 3) link_ALPHA1-2 : angle 1.47511 ( 9) link_ALPHA1-3 : bond 0.00630 ( 9) link_ALPHA1-3 : angle 3.18565 ( 27) link_ALPHA1-6 : bond 0.00553 ( 9) link_ALPHA1-6 : angle 2.51872 ( 27) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 1.95721 ( 45) link_NAG-ASN : bond 0.00763 ( 18) link_NAG-ASN : angle 2.85314 ( 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 310 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9069 (mm-30) REVERT: A 189 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 211 GLN cc_start: 0.8782 (tt0) cc_final: 0.8537 (tt0) REVERT: B 27 GLN cc_start: 0.8210 (tt0) cc_final: 0.7829 (tp-100) REVERT: B 38 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (mm) REVERT: C 31 ASP cc_start: 0.8670 (m-30) cc_final: 0.8454 (m-30) REVERT: D 11 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: D 72 GLU cc_start: 0.8679 (pm20) cc_final: 0.8278 (pm20) REVERT: D 150 GLU cc_start: 0.8427 (pp20) cc_final: 0.8044 (tm-30) REVERT: F 27 GLN cc_start: 0.8071 (tp40) cc_final: 0.7747 (tm-30) REVERT: F 72 GLU cc_start: 0.8688 (pm20) cc_final: 0.8459 (pm20) REVERT: G 87 ASP cc_start: 0.8253 (t0) cc_final: 0.7993 (t70) REVERT: G 154 LYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5644 (mtmt) REVERT: G 174 LYS cc_start: 0.6787 (pttm) cc_final: 0.6373 (mtmm) REVERT: H 82 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: H 181 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: I 20 ILE cc_start: 0.9058 (mt) cc_final: 0.8764 (mp) REVERT: I 55 ASN cc_start: 0.8702 (t0) cc_final: 0.8467 (t0) REVERT: I 107 LYS cc_start: 0.8326 (tptp) cc_final: 0.8125 (tptt) REVERT: J 82 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: J 212 PRO cc_start: 0.8573 (Cg_exo) cc_final: 0.8314 (Cg_endo) REVERT: K 63 ARG cc_start: 0.7321 (ptt-90) cc_final: 0.7094 (ptt-90) REVERT: K 81 GLN cc_start: 0.7185 (mt0) cc_final: 0.6780 (mp10) REVERT: K 165 GLN cc_start: 0.7286 (mm-40) cc_final: 0.7011 (mm-40) REVERT: L 62 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8645 (mmtt) outliers start: 54 outliers final: 26 residues processed: 286 average time/residue: 0.7137 time to fit residues: 229.3512 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 : 0.913 ------------------------------------------------------------------------------- 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 11 GLU 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 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 G residue 154 LYS 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: 0.0070 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 163 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 172 GLN D 34 GLN D 78 GLN D 105 GLN F 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.096273 restraints weight = 28472.605| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.01 r_work: 0.2794 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 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 = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22092 Z= 0.196 Angle : 0.682 12.506 30108 Z= 0.330 Chirality : 0.049 0.364 3507 Planarity : 0.004 0.047 3777 Dihedral : 9.633 70.588 3981 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.57 % Allowed : 12.84 % Favored : 84.60 % 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 aren not related in a simple way. whole: -0.28 (0.16), residues: 2670 helix: 2.55 (0.26), residues: 366 sheet: -0.10 (0.17), residues: 891 loop : -0.98 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 321 TYR 0.013 0.002 TYR D 162 PHE 0.013 0.002 PHE F 9 TRP 0.014 0.002 TRP H 47 HIS 0.015 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00451 (22008) covalent geometry : angle 0.64675 (29886) SS BOND : bond 0.00589 ( 30) SS BOND : angle 2.61501 ( 60) hydrogen bonds : bond 0.03644 ( 862) hydrogen bonds : angle 5.64973 ( 2283) link_ALPHA1-2 : bond 0.00285 ( 3) link_ALPHA1-2 : angle 1.46540 ( 9) link_ALPHA1-3 : bond 0.00664 ( 9) link_ALPHA1-3 : angle 3.18965 ( 27) link_ALPHA1-6 : bond 0.00625 ( 9) link_ALPHA1-6 : angle 2.54539 ( 27) link_BETA1-4 : bond 0.00324 ( 15) link_BETA1-4 : angle 1.93897 ( 45) link_NAG-ASN : bond 0.00709 ( 18) link_NAG-ASN : angle 2.88182 ( 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 310 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9071 (mm-30) REVERT: A 189 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 219 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8894 (m) REVERT: B 27 GLN cc_start: 0.8264 (tt0) cc_final: 0.7858 (tp-100) REVERT: B 38 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8583 (mm) REVERT: C 31 ASP cc_start: 0.8641 (m-30) cc_final: 0.8396 (m-30) REVERT: C 209 SER cc_start: 0.8979 (p) cc_final: 0.8564 (m) REVERT: C 216 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8065 (p0) REVERT: D 72 GLU cc_start: 0.8719 (pm20) cc_final: 0.8302 (pm20) REVERT: D 78 GLN cc_start: 0.9168 (tt0) cc_final: 0.8700 (tt0) REVERT: D 81 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8688 (mt-10) REVERT: D 150 GLU cc_start: 0.8438 (pp20) cc_final: 0.7999 (tm-30) REVERT: E 189 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8171 (tm-30) REVERT: F 27 GLN cc_start: 0.8102 (tp40) cc_final: 0.7786 (tm-30) REVERT: F 72 GLU cc_start: 0.8699 (pm20) cc_final: 0.8447 (pm20) REVERT: G 87 ASP cc_start: 0.8269 (t0) cc_final: 0.7990 (t70) REVERT: G 154 LYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5567 (mtmt) REVERT: G 174 LYS cc_start: 0.6846 (pttm) cc_final: 0.6425 (mtmm) REVERT: H 82 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: I 20 ILE cc_start: 0.9069 (mt) cc_final: 0.8808 (mp) REVERT: I 36 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6900 (m-70) REVERT: I 55 ASN cc_start: 0.8679 (t0) cc_final: 0.8434 (t0) REVERT: J 82 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: J 212 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8315 (Cg_endo) REVERT: K 81 GLN cc_start: 0.7200 (mt0) cc_final: 0.6881 (mp10) REVERT: K 165 GLN cc_start: 0.7290 (mm-40) cc_final: 0.7019 (mm-40) REVERT: L 62 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8761 (mmtt) outliers start: 60 outliers final: 27 residues processed: 285 average time/residue: 0.7362 time to fit residues: 234.5225 Evaluate side-chains 260 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 216 ASN 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 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 49 LEU 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 14 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 211 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3711 r_free = 0.3711 target = 0.142248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096275 restraints weight = 28289.090| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.30 r_work: 0.2796 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 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 = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22092 Z= 0.193 Angle : 0.695 16.565 30108 Z= 0.336 Chirality : 0.050 0.350 3507 Planarity : 0.004 0.047 3777 Dihedral : 9.355 66.843 3981 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.57 % Allowed : 13.99 % Favored : 83.44 % 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 aren not related in a simple way. whole: -0.28 (0.16), residues: 2670 helix: 2.52 (0.26), residues: 366 sheet: -0.06 (0.17), residues: 885 loop : -1.00 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.013 0.002 TYR C 195 PHE 0.016 0.002 PHE F 9 TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00447 (22008) covalent geometry : angle 0.65912 (29886) SS BOND : bond 0.00568 ( 30) SS BOND : angle 2.84520 ( 60) hydrogen bonds : bond 0.03583 ( 862) hydrogen bonds : angle 5.57667 ( 2283) link_ALPHA1-2 : bond 0.00299 ( 3) link_ALPHA1-2 : angle 1.45779 ( 9) link_ALPHA1-3 : bond 0.00689 ( 9) link_ALPHA1-3 : angle 3.16489 ( 27) link_ALPHA1-6 : bond 0.00681 ( 9) link_ALPHA1-6 : angle 2.49335 ( 27) link_BETA1-4 : bond 0.00323 ( 15) link_BETA1-4 : angle 1.88705 ( 45) link_NAG-ASN : bond 0.00714 ( 18) link_NAG-ASN : angle 2.88070 ( 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 299 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9055 (mm-30) REVERT: A 189 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 190 GLU cc_start: 0.8741 (tt0) cc_final: 0.8519 (tt0) REVERT: A 219 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8868 (m) REVERT: B 27 GLN cc_start: 0.8282 (tt0) cc_final: 0.7926 (tp-100) REVERT: B 38 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8598 (mm) REVERT: C 31 ASP cc_start: 0.8667 (m-30) cc_final: 0.8434 (m-30) REVERT: C 195 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: C 209 SER cc_start: 0.8975 (p) cc_final: 0.8576 (m) REVERT: C 216 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8051 (p0) REVERT: C 321 ARG cc_start: 0.9055 (ttt90) cc_final: 0.8809 (ttt-90) REVERT: D 11 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8273 (pp20) REVERT: D 72 GLU cc_start: 0.8721 (pm20) cc_final: 0.8298 (pm20) REVERT: D 74 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: D 78 GLN cc_start: 0.9146 (tt0) cc_final: 0.8854 (tt0) REVERT: D 81 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8701 (mt-10) REVERT: D 150 GLU cc_start: 0.8465 (pp20) cc_final: 0.8089 (tm-30) REVERT: E 189 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8153 (tm-30) REVERT: E 190 GLU cc_start: 0.8784 (tt0) cc_final: 0.8558 (pt0) REVERT: F 27 GLN cc_start: 0.8095 (tp40) cc_final: 0.7789 (tm-30) REVERT: G 87 ASP cc_start: 0.8262 (t0) cc_final: 0.7982 (t70) REVERT: G 154 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.5763 (mttt) REVERT: G 174 LYS cc_start: 0.6838 (pttm) cc_final: 0.6430 (mtmm) REVERT: I 20 ILE cc_start: 0.9069 (mt) cc_final: 0.8805 (mp) REVERT: I 55 ASN cc_start: 0.8675 (t0) cc_final: 0.8404 (t0) REVERT: J 82 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: J 212 PRO cc_start: 0.8620 (Cg_exo) cc_final: 0.8359 (Cg_endo) REVERT: K 81 GLN cc_start: 0.7366 (mt0) cc_final: 0.6923 (mp10) REVERT: K 165 GLN cc_start: 0.7267 (mm-40) cc_final: 0.7026 (mm-40) REVERT: L 62 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8775 (mmtt) outliers start: 60 outliers final: 31 residues processed: 275 average time/residue: 0.7449 time to fit residues: 229.7204 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 : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 SER 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 216 ASN 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 D residue 74 GLU Chi-restraints excluded: chain D residue 81 GLU 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 G residue 154 LYS 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: 0.0670 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 92 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 147 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 overall best weight: 1.0326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 172 GLN D 34 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 36 HIS 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 = 0.3713 r_free = 0.3713 target = 0.142435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096428 restraints weight = 28288.258| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.24 r_work: 0.2801 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22092 Z= 0.192 Angle : 0.686 14.974 30108 Z= 0.331 Chirality : 0.049 0.364 3507 Planarity : 0.004 0.047 3777 Dihedral : 9.119 63.809 3981 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.87 % Allowed : 14.38 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 2670 helix: 2.53 (0.26), residues: 366 sheet: -0.03 (0.17), residues: 882 loop : -1.00 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 321 TYR 0.013 0.002 TYR E 195 PHE 0.016 0.002 PHE B 24 TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS F 64 Details of bonding type rmsd covalent geometry : bond 0.00445 (22008) covalent geometry : angle 0.65269 (29886) SS BOND : bond 0.00633 ( 30) SS BOND : angle 2.49446 ( 60) hydrogen bonds : bond 0.03560 ( 862) hydrogen bonds : angle 5.52106 ( 2283) link_ALPHA1-2 : bond 0.00323 ( 3) link_ALPHA1-2 : angle 1.46149 ( 9) link_ALPHA1-3 : bond 0.00697 ( 9) link_ALPHA1-3 : angle 3.13905 ( 27) link_ALPHA1-6 : bond 0.00704 ( 9) link_ALPHA1-6 : angle 2.44809 ( 27) link_BETA1-4 : bond 0.00334 ( 15) link_BETA1-4 : angle 1.85546 ( 45) link_NAG-ASN : bond 0.00721 ( 18) link_NAG-ASN : angle 2.86135 ( 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 310 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9118 (mm-30) REVERT: A 189 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 190 GLU cc_start: 0.8743 (tt0) cc_final: 0.8532 (tt0) REVERT: A 219 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8831 (m) REVERT: B 27 GLN cc_start: 0.8320 (tt0) cc_final: 0.7987 (tp-100) REVERT: B 38 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 31 ASP cc_start: 0.8670 (m-30) cc_final: 0.8422 (m-30) REVERT: C 195 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: C 209 SER cc_start: 0.8877 (p) cc_final: 0.8557 (m) REVERT: C 216 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8087 (p0) REVERT: D 62 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9097 (mptt) REVERT: D 72 GLU cc_start: 0.8739 (pm20) cc_final: 0.8320 (pm20) REVERT: D 78 GLN cc_start: 0.9156 (tt0) cc_final: 0.8808 (tt0) REVERT: D 81 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: D 150 GLU cc_start: 0.8460 (pp20) cc_final: 0.8081 (tm-30) REVERT: E 189 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 190 GLU cc_start: 0.8778 (tt0) cc_final: 0.8537 (pt0) REVERT: F 27 GLN cc_start: 0.8114 (tp40) cc_final: 0.7751 (tm-30) REVERT: G 87 ASP cc_start: 0.8248 (t0) cc_final: 0.7933 (t70) REVERT: G 154 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5761 (mttt) REVERT: G 174 LYS cc_start: 0.6848 (pttm) cc_final: 0.6448 (mtmm) REVERT: G 184 LEU cc_start: 0.7196 (pt) cc_final: 0.6956 (tp) REVERT: I 20 ILE cc_start: 0.9054 (mt) cc_final: 0.8797 (mp) REVERT: I 55 ASN cc_start: 0.8652 (t0) cc_final: 0.8401 (t0) REVERT: J 82 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: K 63 ARG cc_start: 0.7349 (ptt-90) cc_final: 0.7021 (ptt90) REVERT: K 81 GLN cc_start: 0.7315 (mt0) cc_final: 0.7020 (mm-40) REVERT: L 62 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8775 (mmtt) outliers start: 67 outliers final: 32 residues processed: 288 average time/residue: 0.7267 time to fit residues: 235.8995 Evaluate side-chains 272 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 SER 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 216 ASN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 71 SER 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 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 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 H residue 221 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 128 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 60 ASN B 172 GLN D 34 GLN F 34 GLN F 60 ASN F 78 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098696 restraints weight = 28928.368| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.82 r_work: 0.2833 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22092 Z= 0.135 Angle : 0.654 12.529 30108 Z= 0.316 Chirality : 0.048 0.342 3507 Planarity : 0.004 0.046 3777 Dihedral : 8.677 59.295 3981 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.70 % Allowed : 14.72 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2670 helix: 2.62 (0.26), residues: 366 sheet: -0.09 (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 0.017 0.001 PHE B 24 TRP 0.013 0.001 TRP H 47 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00305 (22008) covalent geometry : angle 0.62400 (29886) SS BOND : bond 0.00487 ( 30) SS BOND : angle 2.15793 ( 60) hydrogen bonds : bond 0.03296 ( 862) hydrogen bonds : angle 5.39406 ( 2283) link_ALPHA1-2 : bond 0.00388 ( 3) link_ALPHA1-2 : angle 1.43840 ( 9) link_ALPHA1-3 : bond 0.00698 ( 9) link_ALPHA1-3 : angle 3.05613 ( 27) link_ALPHA1-6 : bond 0.00705 ( 9) link_ALPHA1-6 : angle 2.35911 ( 27) link_BETA1-4 : bond 0.00323 ( 15) link_BETA1-4 : angle 1.67158 ( 45) link_NAG-ASN : bond 0.00687 ( 18) link_NAG-ASN : angle 2.75125 ( 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 317 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.8811 (tp) REVERT: A 82 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9087 (mm-30) REVERT: A 189 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8005 (tm-30) REVERT: B 27 GLN cc_start: 0.8234 (tt0) cc_final: 0.7931 (tp-100) REVERT: B 38 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8599 (mm) REVERT: C 31 ASP cc_start: 0.8679 (m-30) cc_final: 0.8431 (m-30) REVERT: C 195 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: C 209 SER cc_start: 0.8847 (p) cc_final: 0.8522 (m) REVERT: C 216 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8111 (p0) REVERT: D 72 GLU cc_start: 0.8715 (pm20) cc_final: 0.8176 (pm20) REVERT: E 189 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8202 (tm-30) REVERT: E 190 GLU cc_start: 0.8805 (tt0) cc_final: 0.8550 (pt0) REVERT: F 27 GLN cc_start: 0.8098 (tp40) cc_final: 0.7779 (tm-30) REVERT: F 133 MET cc_start: 0.8797 (mtm) cc_final: 0.8575 (mtm) REVERT: G 87 ASP cc_start: 0.8203 (t0) cc_final: 0.7897 (t70) REVERT: G 154 LYS cc_start: 0.6278 (mmpt) cc_final: 0.5670 (mttt) REVERT: G 174 LYS cc_start: 0.6829 (pttm) cc_final: 0.6422 (mtmm) REVERT: G 184 LEU cc_start: 0.7124 (pt) cc_final: 0.6822 (tp) REVERT: I 20 ILE cc_start: 0.9024 (mt) cc_final: 0.8764 (mp) REVERT: I 55 ASN cc_start: 0.8523 (t0) cc_final: 0.8277 (t0) REVERT: K 63 ARG cc_start: 0.7460 (ptt-90) cc_final: 0.7030 (ptt-90) REVERT: K 81 GLN cc_start: 0.7241 (mt0) cc_final: 0.7008 (mm-40) REVERT: L 62 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8748 (tmtt) outliers start: 63 outliers final: 34 residues processed: 296 average time/residue: 0.6746 time to fit residues: 224.6140 Evaluate side-chains 275 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 C residue 195 TYR Chi-restraints excluded: chain C residue 216 ASN 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 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 36 HIS 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 102 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain I residue 111 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 0.0270 chunk 184 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 226 optimal weight: 0.0030 chunk 173 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 245 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.9652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 172 GLN D 34 GLN D 78 GLN D 168 ASN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100208 restraints weight = 29218.549| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.16 r_work: 0.2796 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 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 = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22092 Z= 0.183 Angle : 0.688 15.157 30108 Z= 0.331 Chirality : 0.049 0.334 3507 Planarity : 0.004 0.046 3777 Dihedral : 8.539 59.960 3981 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.57 % Allowed : 15.19 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.16), residues: 2670 helix: 2.61 (0.26), residues: 366 sheet: -0.11 (0.17), residues: 918 loop : -0.91 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 38 TYR 0.013 0.001 TYR D 162 PHE 0.016 0.002 PHE B 24 TRP 0.013 0.002 TRP G 37 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00424 (22008) covalent geometry : angle 0.65754 (29886) SS BOND : bond 0.00551 ( 30) SS BOND : angle 2.42567 ( 60) hydrogen bonds : bond 0.03462 ( 862) hydrogen bonds : angle 5.40645 ( 2283) link_ALPHA1-2 : bond 0.00329 ( 3) link_ALPHA1-2 : angle 1.46061 ( 9) link_ALPHA1-3 : bond 0.00696 ( 9) link_ALPHA1-3 : angle 3.07169 ( 27) link_ALPHA1-6 : bond 0.00702 ( 9) link_ALPHA1-6 : angle 2.30859 ( 27) link_BETA1-4 : bond 0.00349 ( 15) link_BETA1-4 : angle 1.75423 ( 45) link_NAG-ASN : bond 0.00677 ( 18) link_NAG-ASN : angle 2.81364 ( 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 300 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8846 (tp) REVERT: A 82 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9115 (mm-30) REVERT: A 189 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 219 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8748 (m) REVERT: B 27 GLN cc_start: 0.8274 (tt0) cc_final: 0.8013 (tp-100) REVERT: B 38 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8626 (mm) REVERT: C 31 ASP cc_start: 0.8749 (m-30) cc_final: 0.8506 (m-30) REVERT: C 195 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: C 209 SER cc_start: 0.8919 (p) cc_final: 0.8586 (m) REVERT: C 216 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8143 (p0) REVERT: D 11 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8362 (pp20) REVERT: D 72 GLU cc_start: 0.8705 (pm20) cc_final: 0.8187 (pm20) REVERT: E 189 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8259 (tm-30) REVERT: E 190 GLU cc_start: 0.8836 (tt0) cc_final: 0.8565 (pt0) REVERT: F 27 GLN cc_start: 0.8175 (tp40) cc_final: 0.7868 (tm-30) REVERT: G 87 ASP cc_start: 0.8280 (t0) cc_final: 0.7982 (t70) REVERT: G 154 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5674 (mttt) REVERT: G 174 LYS cc_start: 0.6658 (pttm) cc_final: 0.6251 (mtmm) REVERT: G 184 LEU cc_start: 0.7164 (pt) cc_final: 0.6856 (tp) REVERT: H 181 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: I 20 ILE cc_start: 0.9046 (mt) cc_final: 0.8806 (mp) REVERT: I 36 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6812 (m90) REVERT: I 55 ASN cc_start: 0.8561 (t0) cc_final: 0.8337 (t0) REVERT: J 82 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: K 63 ARG cc_start: 0.7468 (ptt-90) cc_final: 0.6985 (ptt-90) REVERT: K 81 GLN cc_start: 0.7346 (mt0) cc_final: 0.7053 (mm-40) REVERT: L 62 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8788 (mmtt) outliers start: 60 outliers final: 34 residues processed: 279 average time/residue: 0.6877 time to fit residues: 216.0878 Evaluate side-chains 277 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain B residue 38 LEU 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 C residue 216 ASN 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 E residue 13 LEU 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 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 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 154 LYS 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 H residue 181 GLN Chi-restraints excluded: chain H residue 221 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 40 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 176 optimal weight: 0.0570 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 172 GLN D 34 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 36 HIS H 43 GLN H 181 GLN I 36 HIS I 91 GLN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099753 restraints weight = 29120.643| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.12 r_work: 0.2800 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 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 = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22092 Z= 0.156 Angle : 0.678 15.249 30108 Z= 0.326 Chirality : 0.048 0.336 3507 Planarity : 0.004 0.046 3777 Dihedral : 8.272 59.358 3981 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.40 % Allowed : 15.66 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2670 helix: 2.63 (0.26), residues: 366 sheet: -0.02 (0.17), residues: 888 loop : -0.83 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 57 TYR 0.016 0.001 TYR D 162 PHE 0.016 0.001 PHE B 24 TRP 0.013 0.001 TRP L 47 HIS 0.007 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00358 (22008) covalent geometry : angle 0.64670 (29886) SS BOND : bond 0.00501 ( 30) SS BOND : angle 2.58238 ( 60) hydrogen bonds : bond 0.03374 ( 862) hydrogen bonds : angle 5.35328 ( 2283) link_ALPHA1-2 : bond 0.00358 ( 3) link_ALPHA1-2 : angle 1.45200 ( 9) link_ALPHA1-3 : bond 0.00694 ( 9) link_ALPHA1-3 : angle 3.03463 ( 27) link_ALPHA1-6 : bond 0.00683 ( 9) link_ALPHA1-6 : angle 2.21747 ( 27) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 1.67751 ( 45) link_NAG-ASN : bond 0.00650 ( 18) link_NAG-ASN : angle 2.77935 ( 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: 56 poor density : 238 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.8828 (tp) REVERT: A 82 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9120 (mm-30) REVERT: A 123 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8494 (mt-10) REVERT: A 189 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 219 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8728 (m) REVERT: B 11 GLU cc_start: 0.8521 (pp20) cc_final: 0.8265 (tm-30) REVERT: B 27 GLN cc_start: 0.8267 (tt0) cc_final: 0.8008 (tp-100) REVERT: B 38 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8623 (mm) REVERT: C 31 ASP cc_start: 0.8797 (m-30) cc_final: 0.8567 (m-30) REVERT: C 195 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: C 209 SER cc_start: 0.8983 (p) cc_final: 0.8657 (m) REVERT: C 216 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8142 (p0) REVERT: D 72 GLU cc_start: 0.8702 (pm20) cc_final: 0.8175 (pm20) REVERT: E 189 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8260 (tm-30) REVERT: E 190 GLU cc_start: 0.8834 (tt0) cc_final: 0.8563 (pt0) REVERT: F 27 GLN cc_start: 0.8164 (tp40) cc_final: 0.7857 (tm-30) REVERT: F 133 MET cc_start: 0.8769 (mtm) cc_final: 0.8551 (mtm) REVERT: G 87 ASP cc_start: 0.8229 (t0) cc_final: 0.7990 (t70) REVERT: G 154 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5675 (mttt) REVERT: G 174 LYS cc_start: 0.6511 (pttm) cc_final: 0.6138 (mtmm) REVERT: G 184 LEU cc_start: 0.7175 (pt) cc_final: 0.6868 (tp) REVERT: I 20 ILE cc_start: 0.9051 (mt) cc_final: 0.8834 (mp) REVERT: J 82 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: K 63 ARG cc_start: 0.7495 (ptt-90) cc_final: 0.7157 (ptt-90) REVERT: K 81 GLN cc_start: 0.7253 (mt0) cc_final: 0.6979 (mm-40) REVERT: L 62 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8789 (tmtt) outliers start: 56 outliers final: 36 residues processed: 273 average time/residue: 0.6860 time to fit residues: 210.9808 Evaluate side-chains 271 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain B residue 38 LEU 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 C residue 216 ASN 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 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 36 HIS 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 G residue 154 LYS 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 123 THR Chi-restraints excluded: chain H residue 221 VAL 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 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: 0.9980 chunk 130 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 106 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 147 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3723 r_free = 0.3723 target = 0.142771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099857 restraints weight = 29145.936| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.13 r_work: 0.2806 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 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 = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22092 Z= 0.173 Angle : 0.684 14.777 30108 Z= 0.330 Chirality : 0.049 0.335 3507 Planarity : 0.004 0.046 3777 Dihedral : 8.152 59.656 3981 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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 aren not related in a simple way. whole: -0.13 (0.16), residues: 2670 helix: 2.63 (0.26), residues: 366 sheet: -0.03 (0.17), residues: 888 loop : -0.84 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 57 TYR 0.015 0.001 TYR D 162 PHE 0.017 0.002 PHE F 9 TRP 0.014 0.002 TRP H 47 HIS 0.027 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00401 (22008) covalent geometry : angle 0.65352 (29886) SS BOND : bond 0.00498 ( 30) SS BOND : angle 2.53574 ( 60) hydrogen bonds : bond 0.03424 ( 862) hydrogen bonds : angle 5.34576 ( 2283) link_ALPHA1-2 : bond 0.00326 ( 3) link_ALPHA1-2 : angle 1.45039 ( 9) link_ALPHA1-3 : bond 0.00700 ( 9) link_ALPHA1-3 : angle 3.03544 ( 27) link_ALPHA1-6 : bond 0.00681 ( 9) link_ALPHA1-6 : angle 2.18078 ( 27) link_BETA1-4 : bond 0.00367 ( 15) link_BETA1-4 : angle 1.68762 ( 45) link_NAG-ASN : bond 0.00662 ( 18) link_NAG-ASN : angle 2.79349 ( 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 282 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.8854 (tp) REVERT: A 82 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9113 (mm-30) REVERT: A 189 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 219 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8718 (m) REVERT: B 11 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: B 27 GLN cc_start: 0.8263 (tt0) cc_final: 0.7976 (tp-100) REVERT: B 38 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8618 (mm) REVERT: C 31 ASP cc_start: 0.8730 (m-30) cc_final: 0.8482 (m-30) REVERT: C 195 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: C 209 SER cc_start: 0.8966 (p) cc_final: 0.8631 (m) REVERT: C 216 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8151 (p0) REVERT: D 71 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8896 (p) REVERT: D 72 GLU cc_start: 0.8687 (pm20) cc_final: 0.8019 (pm20) REVERT: E 189 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8230 (tm-30) REVERT: E 190 GLU cc_start: 0.8838 (tt0) cc_final: 0.8535 (pt0) REVERT: F 27 GLN cc_start: 0.8160 (tp40) cc_final: 0.7845 (tm-30) REVERT: G 87 ASP cc_start: 0.8272 (t0) cc_final: 0.7989 (t70) REVERT: G 154 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5668 (mttt) REVERT: G 174 LYS cc_start: 0.6514 (pttm) cc_final: 0.6141 (mtmm) REVERT: G 184 LEU cc_start: 0.7215 (pt) cc_final: 0.6966 (tp) REVERT: I 20 ILE cc_start: 0.9051 (mt) cc_final: 0.8822 (mp) REVERT: J 82 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: K 63 ARG cc_start: 0.7479 (ptt-90) cc_final: 0.7131 (ptt-90) REVERT: K 81 GLN cc_start: 0.7227 (mt0) cc_final: 0.6948 (mm-40) REVERT: L 62 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8777 (tmtt) outliers start: 55 outliers final: 33 residues processed: 261 average time/residue: 0.7148 time to fit residues: 210.1531 Evaluate side-chains 266 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 38 LEU 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 C residue 216 ASN 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 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 138 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 154 LYS 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 H residue 221 VAL 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 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: 9.9990 chunk 164 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 172 GLN D 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089538 restraints weight = 29238.724| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.05 r_work: 0.2841 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- 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: 5 | |-----------------------------------------------------------------------------| |-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: 5 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22092 Z= 0.209 Angle : 0.703 14.996 30108 Z= 0.339 Chirality : 0.049 0.331 3507 Planarity : 0.005 0.051 3777 Dihedral : 8.123 59.759 3981 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.35 % Allowed : 15.92 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2670 helix: 2.58 (0.26), residues: 366 sheet: -0.09 (0.17), residues: 900 loop : -0.96 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 0.005 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00486 (22008) covalent geometry : angle 0.67272 (29886) SS BOND : bond 0.00549 ( 30) SS BOND : angle 2.58331 ( 60) hydrogen bonds : bond 0.03569 ( 862) hydrogen bonds : angle 5.38618 ( 2283) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 1.46356 ( 9) link_ALPHA1-3 : bond 0.00693 ( 9) link_ALPHA1-3 : angle 3.04427 ( 27) link_ALPHA1-6 : bond 0.00677 ( 9) link_ALPHA1-6 : angle 2.14854 ( 27) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 1.75596 ( 45) link_NAG-ASN : bond 0.00709 ( 18) link_NAG-ASN : angle 2.84293 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10612.78 seconds wall clock time: 181 minutes 16.96 seconds (10876.96 seconds total)