Starting phenix.real_space_refine on Sat Aug 23 12:35:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uad_42060/08_2025/8uad_42060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uad_42060/08_2025/8uad_42060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uad_42060/08_2025/8uad_42060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uad_42060/08_2025/8uad_42060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uad_42060/08_2025/8uad_42060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uad_42060/08_2025/8uad_42060.map" } resolution = 2.77 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= 0.077 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 63 5.16 5 C 7722 2.51 5 N 2073 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12318 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "B" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "C" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "E" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "F" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" 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: "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: "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: "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 Time building chain proxies: 3.19, per 1000 atoms: 0.26 Number of scatterers: 12318 At special positions: 0 Unit cell: (95.55, 93.73, 144.69, 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 63 16.00 O 2460 8.00 N 2073 7.00 C 7722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.02 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.05 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.02 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 272 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 318 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 57 " distance=2.05 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 143 " distance=2.02 Simple disulfide: pdb=" SG CYS E 178 " - pdb=" SG CYS E 272 " distance=2.04 Simple disulfide: pdb=" SG CYS E 292 " - pdb=" SG CYS E 318 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 59 " " NAG A 402 " - " ASN A 230 " " NAG C 401 " - " ASN C 59 " " NAG C 402 " - " ASN C 230 " " NAG E 401 " - " ASN E 59 " " NAG E 402 " - " ASN E 230 " " NAG G 1 " - " ASN A 330 " " NAG H 1 " - " ASN A 301 " " NAG I 1 " - " ASN A 25 " " NAG J 1 " - " ASN A 194 " " NAG K 1 " - " ASN A 145 " " NAG L 1 " - " ASN C 330 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 25 " " NAG O 1 " - " ASN C 194 " " NAG P 1 " - " ASN C 145 " " NAG Q 1 " - " ASN E 330 " " NAG R 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 25 " " NAG T 1 " - " ASN E 194 " " NAG U 1 " - " ASN E 145 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 553.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 27.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.549A pdb=" N ARG A 101 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.527A pdb=" N GLY A 129 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.535A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 removed outlier: 3.999A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 110 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.550A pdb=" N ARG C 101 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 102 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.528A pdb=" N GLY C 129 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.536A pdb=" N LYS C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE D 6 " --> pdb=" O PHE D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 removed outlier: 3.999A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.549A pdb=" N ARG E 101 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 102 " --> pdb=" O HIS E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 126 through 130 removed outlier: 3.527A pdb=" N GLY E 129 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.536A pdb=" N LYS E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE F 6 " --> pdb=" O PHE F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 57 removed outlier: 4.000A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 110 Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU F 118 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.554A pdb=" N VAL B 131 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN A 43 " --> pdb=" O ALA A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE A 280 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.494A pdb=" N VAL A 187 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE A 264 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'A' and resid 170 through 174 Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AB1, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.555A pdb=" N VAL D 131 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN C 43 " --> pdb=" O ALA C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE C 280 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.494A pdb=" N VAL C 187 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE C 264 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 174 Processing sheet with id=AC1, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AC2, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.556A pdb=" N VAL F 131 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN E 43 " --> pdb=" O ALA E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE E 280 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 116 through 119 removed outlier: 7.493A pdb=" N VAL E 187 " --> pdb=" O PRO E 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE E 264 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 116 through 119 Processing sheet with id=AD1, first strand: chain 'E' and resid 170 through 174 Processing sheet with id=AD2, first strand: chain 'E' and resid 298 through 300 Processing sheet with id=AD3, first strand: chain 'E' and resid 306 through 307 492 hydrogen bonds defined for protein. 1314 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: 1.75 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3825 1.34 - 1.46: 2773 1.46 - 1.58: 5882 1.58 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 12564 Sorted by residual: bond pdb=" C1 BMA Q 3 " pdb=" C2 BMA Q 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.78e+00 ... (remaining 12559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16108 1.95 - 3.90: 724 3.90 - 5.85: 142 5.85 - 7.80: 45 7.80 - 9.75: 12 Bond angle restraints: 17031 Sorted by residual: angle pdb=" CA CYS C 94 " pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CA CYS A 94 " pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " ideal model delta sigma weight residual 114.40 124.14 -9.74 2.30e+00 1.89e-01 1.79e+01 angle pdb=" CA CYS E 94 " pdb=" CB CYS E 94 " pdb=" SG CYS E 94 " ideal model delta sigma weight residual 114.40 124.12 -9.72 2.30e+00 1.89e-01 1.79e+01 angle pdb=" C GLY C 93 " pdb=" N CYS C 94 " pdb=" CA CYS C 94 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C GLY A 93 " pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 ... (remaining 17026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 7495 22.32 - 44.63: 449 44.63 - 66.95: 90 66.95 - 89.27: 81 89.27 - 111.59: 72 Dihedral angle restraints: 8187 sinusoidal: 3864 harmonic: 4323 Sorted by residual: dihedral pdb=" CA THR C 179 " pdb=" C THR C 179 " pdb=" N GLU C 180 " pdb=" CA GLU C 180 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA THR E 179 " pdb=" C THR E 179 " pdb=" N GLU E 180 " pdb=" CA GLU E 180 " ideal model delta harmonic sigma weight residual 180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" N GLU A 180 " pdb=" CA GLU A 180 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1547 0.062 - 0.123: 426 0.123 - 0.185: 61 0.185 - 0.246: 12 0.246 - 0.308: 18 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CG LEU E 170 " pdb=" CB LEU E 170 " pdb=" CD1 LEU E 170 " pdb=" CD2 LEU E 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CG LEU C 170 " pdb=" CB LEU C 170 " pdb=" CD1 LEU C 170 " pdb=" CD2 LEU C 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2061 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 114 " 0.015 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE F 114 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE F 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 114 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 114 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 114 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 114 " 0.015 2.00e-02 2.50e+03 1.38e-02 3.35e+00 pdb=" CG PHE D 114 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 114 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 114 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 114 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 114 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 114 " -0.015 2.00e-02 2.50e+03 1.38e-02 3.33e+00 pdb=" CG PHE B 114 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 114 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 114 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 114 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 114 " -0.003 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1647 2.75 - 3.29: 10387 3.29 - 3.83: 18809 3.83 - 4.36: 22964 4.36 - 4.90: 41350 Nonbonded interactions: 95157 Sorted by model distance: nonbonded pdb=" OH TYR C 176 " pdb=" O GLU C 182 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR E 176 " pdb=" O GLU E 182 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 176 " pdb=" O GLU A 182 " model vdw 2.217 3.040 nonbonded pdb=" NZ LYS E 38 " pdb=" O SER E 39 " model vdw 2.221 3.120 nonbonded pdb=" NZ LYS C 38 " pdb=" O SER C 39 " model vdw 2.221 3.120 ... (remaining 95152 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: 0.03 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'P' 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=1.00 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.009 0.057 12633 Z= 0.372 Angle : 1.044 9.749 17217 Z= 0.510 Chirality : 0.062 0.308 2064 Planarity : 0.006 0.042 2121 Dihedral : 20.425 111.586 5370 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.71 % Allowed : 0.94 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.82 (0.21), residues: 1521 helix: 0.35 (0.29), residues: 363 sheet: 0.45 (0.29), residues: 294 loop : -1.34 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 335 TYR 0.014 0.003 TYR A 307 PHE 0.033 0.003 PHE F 114 TRP 0.012 0.002 TRP A 188 HIS 0.007 0.002 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00899 (12564) covalent geometry : angle 1.02681 (17031) SS BOND : bond 0.00864 ( 21) SS BOND : angle 2.25091 ( 42) hydrogen bonds : bond 0.15269 ( 468) hydrogen bonds : angle 5.62258 ( 1314) link_BETA1-4 : bond 0.00794 ( 27) link_BETA1-4 : angle 2.04545 ( 81) link_NAG-ASN : bond 0.00621 ( 21) link_NAG-ASN : angle 2.08057 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.505 Fit side-chains REVERT: C 198 MET cc_start: 0.8819 (mmm) cc_final: 0.8521 (mmm) outliers start: 9 outliers final: 1 residues processed: 181 average time/residue: 0.7091 time to fit residues: 137.4781 Evaluate side-chains 111 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.163505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.128344 restraints weight = 12360.759| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.18 r_work: 0.3071 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12633 Z= 0.128 Angle : 0.709 9.102 17217 Z= 0.333 Chirality : 0.046 0.254 2064 Planarity : 0.005 0.037 2121 Dihedral : 15.067 86.899 2611 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 7.23 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.05 (0.21), residues: 1521 helix: 1.52 (0.31), residues: 342 sheet: 0.58 (0.29), residues: 309 loop : -0.92 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.010 0.001 TYR A 307 PHE 0.014 0.002 PHE D 114 TRP 0.004 0.001 TRP D 21 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00266 (12564) covalent geometry : angle 0.68256 (17031) SS BOND : bond 0.00397 ( 21) SS BOND : angle 1.11915 ( 42) hydrogen bonds : bond 0.05300 ( 468) hydrogen bonds : angle 4.87076 ( 1314) link_BETA1-4 : bond 0.00891 ( 27) link_BETA1-4 : angle 2.47876 ( 81) link_NAG-ASN : bond 0.00351 ( 21) link_NAG-ASN : angle 1.63447 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7888 (ptt180) cc_final: 0.7514 (mtp-110) REVERT: B 59 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: C 75 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7660 (mptt) REVERT: C 88 ARG cc_start: 0.7843 (ptt180) cc_final: 0.7507 (mtp-110) REVERT: D 59 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: E 75 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8323 (mptt) REVERT: E 88 ARG cc_start: 0.7823 (ptt180) cc_final: 0.7418 (mtp-110) REVERT: E 248 MET cc_start: 0.9131 (ptt) cc_final: 0.8907 (ptt) outliers start: 15 outliers final: 4 residues processed: 150 average time/residue: 0.6654 time to fit residues: 108.0108 Evaluate side-chains 143 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 63 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.156544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120696 restraints weight = 12450.333| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.07 r_work: 0.2982 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 12633 Z= 0.352 Angle : 0.981 10.137 17217 Z= 0.472 Chirality : 0.059 0.306 2064 Planarity : 0.007 0.052 2121 Dihedral : 12.388 78.853 2607 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.70 % Favored : 97.11 % Rotamer: Outliers : 2.28 % Allowed : 10.61 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.47 (0.21), residues: 1521 helix: 1.00 (0.30), residues: 339 sheet: 0.38 (0.28), residues: 339 loop : -1.19 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 88 TYR 0.016 0.003 TYR E 307 PHE 0.019 0.003 PHE C 190 TRP 0.013 0.003 TRP A 188 HIS 0.009 0.002 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00888 (12564) covalent geometry : angle 0.95623 (17031) SS BOND : bond 0.00981 ( 21) SS BOND : angle 2.77780 ( 42) hydrogen bonds : bond 0.08505 ( 468) hydrogen bonds : angle 4.94459 ( 1314) link_BETA1-4 : bond 0.00754 ( 27) link_BETA1-4 : angle 2.32193 ( 81) link_NAG-ASN : bond 0.00483 ( 21) link_NAG-ASN : angle 1.96830 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8324 (tmtm) cc_final: 0.7740 (mptt) REVERT: B 59 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: D 59 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: D 82 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: E 75 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8489 (mptt) REVERT: F 57 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7391 (pt0) outliers start: 29 outliers final: 14 residues processed: 152 average time/residue: 0.6876 time to fit residues: 112.6451 Evaluate side-chains 150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.161606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125844 restraints weight = 12333.507| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.26 r_work: 0.3037 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12633 Z= 0.144 Angle : 0.703 9.547 17217 Z= 0.336 Chirality : 0.045 0.259 2064 Planarity : 0.005 0.037 2121 Dihedral : 10.431 70.192 2607 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.97 % Allowed : 13.29 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.23 (0.21), residues: 1521 helix: 1.23 (0.30), residues: 360 sheet: 0.49 (0.29), residues: 309 loop : -1.04 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.010 0.001 TYR A 307 PHE 0.014 0.002 PHE C 190 TRP 0.006 0.001 TRP E 188 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00327 (12564) covalent geometry : angle 0.68096 (17031) SS BOND : bond 0.00420 ( 21) SS BOND : angle 1.69968 ( 42) hydrogen bonds : bond 0.05864 ( 468) hydrogen bonds : angle 4.79356 ( 1314) link_BETA1-4 : bond 0.00730 ( 27) link_BETA1-4 : angle 1.97479 ( 81) link_NAG-ASN : bond 0.00343 ( 21) link_NAG-ASN : angle 1.69203 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8255 (tmtm) cc_final: 0.7697 (mptt) REVERT: A 88 ARG cc_start: 0.8091 (ptt180) cc_final: 0.7667 (mtp-110) REVERT: B 59 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: B 132 GLU cc_start: 0.7190 (tt0) cc_final: 0.6838 (pm20) REVERT: C 75 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7746 (mptt) REVERT: D 59 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: E 75 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8438 (mptt) REVERT: F 132 GLU cc_start: 0.7339 (tt0) cc_final: 0.6839 (pm20) outliers start: 25 outliers final: 7 residues processed: 164 average time/residue: 0.6377 time to fit residues: 113.3860 Evaluate side-chains 150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.123945 restraints weight = 12393.106| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.02 r_work: 0.3032 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12633 Z= 0.181 Angle : 0.755 9.800 17217 Z= 0.360 Chirality : 0.048 0.269 2064 Planarity : 0.005 0.041 2121 Dihedral : 9.729 61.961 2607 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 13.99 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.23 (0.21), residues: 1521 helix: 1.28 (0.30), residues: 357 sheet: 0.47 (0.29), residues: 309 loop : -1.05 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.013 0.002 TYR E 307 PHE 0.016 0.002 PHE C 190 TRP 0.008 0.002 TRP E 188 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00434 (12564) covalent geometry : angle 0.73379 (17031) SS BOND : bond 0.00557 ( 21) SS BOND : angle 1.94721 ( 42) hydrogen bonds : bond 0.06342 ( 468) hydrogen bonds : angle 4.76925 ( 1314) link_BETA1-4 : bond 0.00716 ( 27) link_BETA1-4 : angle 1.90862 ( 81) link_NAG-ASN : bond 0.00382 ( 21) link_NAG-ASN : angle 1.68205 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8226 (tmtm) cc_final: 0.7684 (mptt) REVERT: A 88 ARG cc_start: 0.8132 (ptt180) cc_final: 0.7709 (mtp-110) REVERT: B 59 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: B 132 GLU cc_start: 0.7277 (tt0) cc_final: 0.6911 (pm20) REVERT: C 75 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7768 (mptt) REVERT: D 59 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: E 75 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8440 (mptt) REVERT: F 132 GLU cc_start: 0.7304 (tt0) cc_final: 0.6974 (pm20) outliers start: 23 outliers final: 11 residues processed: 153 average time/residue: 0.6205 time to fit residues: 103.2098 Evaluate side-chains 154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.162434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.125693 restraints weight = 12442.256| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.14 r_work: 0.3065 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12633 Z= 0.126 Angle : 0.658 9.611 17217 Z= 0.311 Chirality : 0.044 0.256 2064 Planarity : 0.004 0.035 2121 Dihedral : 8.570 57.552 2607 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.81 % Allowed : 14.54 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.21), residues: 1521 helix: 1.62 (0.30), residues: 357 sheet: 0.48 (0.29), residues: 309 loop : -0.84 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.010 0.001 TYR A 307 PHE 0.013 0.001 PHE C 190 TRP 0.005 0.001 TRP C 271 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00283 (12564) covalent geometry : angle 0.63767 (17031) SS BOND : bond 0.00364 ( 21) SS BOND : angle 1.42727 ( 42) hydrogen bonds : bond 0.05204 ( 468) hydrogen bonds : angle 4.64687 ( 1314) link_BETA1-4 : bond 0.00740 ( 27) link_BETA1-4 : angle 1.87055 ( 81) link_NAG-ASN : bond 0.00337 ( 21) link_NAG-ASN : angle 1.56591 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8228 (tmtm) cc_final: 0.7692 (mptt) REVERT: A 88 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7671 (mtp-110) REVERT: A 289 GLU cc_start: 0.8073 (tt0) cc_final: 0.7845 (mt-10) REVERT: B 132 GLU cc_start: 0.7283 (tt0) cc_final: 0.6923 (pm20) REVERT: C 75 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7750 (mptt) REVERT: E 75 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8397 (mptt) REVERT: E 248 MET cc_start: 0.9139 (ptt) cc_final: 0.8870 (ptt) REVERT: F 132 GLU cc_start: 0.7272 (tt0) cc_final: 0.6895 (pm20) outliers start: 23 outliers final: 12 residues processed: 165 average time/residue: 0.6218 time to fit residues: 111.3349 Evaluate side-chains 155 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 115 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.162556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124839 restraints weight = 12303.674| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.39 r_work: 0.3073 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12633 Z= 0.126 Angle : 0.653 9.650 17217 Z= 0.308 Chirality : 0.044 0.255 2064 Planarity : 0.004 0.037 2121 Dihedral : 7.978 58.369 2607 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.57 % Allowed : 15.64 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.20 (0.22), residues: 1521 helix: 1.75 (0.30), residues: 357 sheet: 0.56 (0.29), residues: 309 loop : -0.75 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.011 0.001 TYR A 307 PHE 0.014 0.001 PHE C 190 TRP 0.005 0.001 TRP C 271 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00281 (12564) covalent geometry : angle 0.63350 (17031) SS BOND : bond 0.00368 ( 21) SS BOND : angle 1.42616 ( 42) hydrogen bonds : bond 0.05097 ( 468) hydrogen bonds : angle 4.60959 ( 1314) link_BETA1-4 : bond 0.00754 ( 27) link_BETA1-4 : angle 1.89253 ( 81) link_NAG-ASN : bond 0.00328 ( 21) link_NAG-ASN : angle 1.50025 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8253 (tmtm) cc_final: 0.7740 (mptt) REVERT: A 88 ARG cc_start: 0.8089 (ptt180) cc_final: 0.7624 (mtp-110) REVERT: A 265 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8588 (mt) REVERT: A 289 GLU cc_start: 0.8086 (tt0) cc_final: 0.7872 (mt-10) REVERT: B 132 GLU cc_start: 0.7275 (tt0) cc_final: 0.6965 (pm20) REVERT: C 75 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7789 (mptt) REVERT: E 75 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8429 (mptt) REVERT: E 248 MET cc_start: 0.9139 (ptt) cc_final: 0.8849 (ptt) REVERT: F 132 GLU cc_start: 0.7255 (tt0) cc_final: 0.6874 (pm20) outliers start: 20 outliers final: 14 residues processed: 155 average time/residue: 0.5636 time to fit residues: 95.2238 Evaluate side-chains 152 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 132 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 142 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.159549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121916 restraints weight = 12288.644| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.10 r_work: 0.3019 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12633 Z= 0.204 Angle : 0.777 9.902 17217 Z= 0.369 Chirality : 0.048 0.267 2064 Planarity : 0.005 0.041 2121 Dihedral : 7.976 59.918 2607 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.59 % Allowed : 15.25 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.21), residues: 1521 helix: 1.40 (0.30), residues: 357 sheet: 0.28 (0.29), residues: 324 loop : -0.90 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 262 TYR 0.013 0.002 TYR C 307 PHE 0.016 0.002 PHE C 190 TRP 0.008 0.002 TRP E 188 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00497 (12564) covalent geometry : angle 0.75494 (17031) SS BOND : bond 0.00620 ( 21) SS BOND : angle 2.16656 ( 42) hydrogen bonds : bond 0.06540 ( 468) hydrogen bonds : angle 4.73169 ( 1314) link_BETA1-4 : bond 0.00742 ( 27) link_BETA1-4 : angle 1.98045 ( 81) link_NAG-ASN : bond 0.00386 ( 21) link_NAG-ASN : angle 1.68290 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8234 (tmtm) cc_final: 0.7714 (mptt) REVERT: A 265 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8598 (mt) REVERT: A 289 GLU cc_start: 0.8119 (tt0) cc_final: 0.7886 (mt-10) REVERT: B 59 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: B 132 GLU cc_start: 0.7287 (tt0) cc_final: 0.6981 (pm20) REVERT: C 75 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7807 (mptt) REVERT: E 75 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8476 (mptt) REVERT: F 132 GLU cc_start: 0.7232 (tt0) cc_final: 0.6899 (pm20) outliers start: 33 outliers final: 15 residues processed: 159 average time/residue: 0.5912 time to fit residues: 102.2252 Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.0170 chunk 87 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.161862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125307 restraints weight = 12286.155| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.23 r_work: 0.3041 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12633 Z= 0.134 Angle : 0.666 9.676 17217 Z= 0.316 Chirality : 0.044 0.259 2064 Planarity : 0.004 0.038 2121 Dihedral : 7.372 58.151 2607 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.12 % Allowed : 15.96 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.11 (0.21), residues: 1521 helix: 1.63 (0.30), residues: 357 sheet: 0.54 (0.29), residues: 309 loop : -0.79 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.011 0.001 TYR E 307 PHE 0.015 0.001 PHE C 190 TRP 0.006 0.001 TRP E 188 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00304 (12564) covalent geometry : angle 0.64344 (17031) SS BOND : bond 0.00383 ( 21) SS BOND : angle 1.86105 ( 42) hydrogen bonds : bond 0.05366 ( 468) hydrogen bonds : angle 4.63749 ( 1314) link_BETA1-4 : bond 0.00737 ( 27) link_BETA1-4 : angle 1.89669 ( 81) link_NAG-ASN : bond 0.00315 ( 21) link_NAG-ASN : angle 1.58130 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8243 (tmtm) cc_final: 0.7683 (mptt) REVERT: A 88 ARG cc_start: 0.8161 (ptt180) cc_final: 0.7643 (mtp-110) REVERT: A 265 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8585 (mt) REVERT: A 289 GLU cc_start: 0.8091 (tt0) cc_final: 0.7876 (mt-10) REVERT: B 59 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: B 132 GLU cc_start: 0.7243 (tt0) cc_final: 0.6936 (pm20) REVERT: C 75 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7752 (mptt) REVERT: E 75 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8456 (mptt) REVERT: F 132 GLU cc_start: 0.7242 (tt0) cc_final: 0.6853 (pm20) outliers start: 27 outliers final: 14 residues processed: 156 average time/residue: 0.6088 time to fit residues: 103.3699 Evaluate side-chains 153 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.160497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.123795 restraints weight = 12368.859| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.17 r_work: 0.3034 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12633 Z= 0.171 Angle : 0.718 9.828 17217 Z= 0.342 Chirality : 0.046 0.264 2064 Planarity : 0.005 0.039 2121 Dihedral : 7.310 59.966 2607 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.97 % Allowed : 16.59 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.04 (0.21), residues: 1521 helix: 1.44 (0.30), residues: 360 sheet: 0.31 (0.29), residues: 324 loop : -0.82 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 112 TYR 0.012 0.002 TYR A 307 PHE 0.016 0.002 PHE C 190 TRP 0.011 0.002 TRP B 14 HIS 0.005 0.001 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00409 (12564) covalent geometry : angle 0.69562 (17031) SS BOND : bond 0.00509 ( 21) SS BOND : angle 2.08546 ( 42) hydrogen bonds : bond 0.06005 ( 468) hydrogen bonds : angle 4.68237 ( 1314) link_BETA1-4 : bond 0.00737 ( 27) link_BETA1-4 : angle 1.88029 ( 81) link_NAG-ASN : bond 0.00356 ( 21) link_NAG-ASN : angle 1.60757 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8227 (tmtm) cc_final: 0.7694 (mptt) REVERT: A 160 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8411 (t) REVERT: A 265 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 289 GLU cc_start: 0.8087 (tt0) cc_final: 0.7855 (mt-10) REVERT: B 59 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: B 132 GLU cc_start: 0.7195 (tt0) cc_final: 0.6927 (pm20) REVERT: C 75 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7765 (mptt) REVERT: E 75 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8455 (mptt) REVERT: E 160 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8512 (t) REVERT: F 132 GLU cc_start: 0.7205 (tt0) cc_final: 0.6859 (pm20) outliers start: 25 outliers final: 15 residues processed: 152 average time/residue: 0.5797 time to fit residues: 96.2825 Evaluate side-chains 157 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.163409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126851 restraints weight = 12299.075| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.08 r_work: 0.3098 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12633 Z= 0.116 Angle : 0.617 9.613 17217 Z= 0.294 Chirality : 0.043 0.255 2064 Planarity : 0.004 0.036 2121 Dihedral : 6.777 57.315 2607 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.81 % Allowed : 16.67 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.22), residues: 1521 helix: 1.79 (0.30), residues: 357 sheet: 0.59 (0.29), residues: 309 loop : -0.70 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 120 TYR 0.009 0.001 TYR A 307 PHE 0.014 0.001 PHE C 190 TRP 0.004 0.001 TRP C 271 HIS 0.004 0.001 HIS C 294 Details of bonding type rmsd covalent geometry : bond 0.00257 (12564) covalent geometry : angle 0.59594 (17031) SS BOND : bond 0.00317 ( 21) SS BOND : angle 1.59792 ( 42) hydrogen bonds : bond 0.04805 ( 468) hydrogen bonds : angle 4.56887 ( 1314) link_BETA1-4 : bond 0.00744 ( 27) link_BETA1-4 : angle 1.78612 ( 81) link_NAG-ASN : bond 0.00320 ( 21) link_NAG-ASN : angle 1.50555 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4562.88 seconds wall clock time: 78 minutes 43.93 seconds (4723.93 seconds total)