Starting phenix.real_space_refine on Thu Sep 18 05:08:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ff1_50348/09_2025/9ff1_50348.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ff1_50348/09_2025/9ff1_50348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ff1_50348/09_2025/9ff1_50348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ff1_50348/09_2025/9ff1_50348.map" model { file = "/net/cci-nas-00/data/ceres_data/9ff1_50348/09_2025/9ff1_50348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ff1_50348/09_2025/9ff1_50348.cif" } resolution = 3.2 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= 0.003 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 80 5.16 5 C 9361 2.51 5 N 2302 2.21 5 O 2647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14390 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2823 Chain: "B" Number of atoms: 2774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2812 Chain: "C" Number of atoms: 2765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2823 Chain: "D" Number of atoms: 2774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2812 Chain: "E" Number of atoms: 2765 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 337, 2757 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 320} bond proxies already assigned to first conformer: 2823 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'HSM': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N AASN B 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 41 " occ=0.50 residue: pdb=" N AASN C 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 41 " occ=0.50 residue: pdb=" N AASN D 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 41 " occ=0.50 residue: pdb=" N AASN E 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 41 " occ=0.50 Time building chain proxies: 5.67, per 1000 atoms: 0.39 Number of scatterers: 14390 At special positions: 0 Unit cell: (99.1936, 100.434, 130.192, 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 80 16.00 O 2647 8.00 N 2302 7.00 C 9361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 501 " - " ASN A 8 " " NAG B 502 " - " ASN B 8 " " NAG C 501 " - " ASN C 8 " " NAG D 502 " - " ASN D 8 " " NAG E 501 " - " ASN E 8 " " NAG F 1 " - " ASN A 80 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN C 80 " " NAG I 1 " - " ASN D 80 " " NAG J 1 " - " ASN E 80 " " NAG a 1 " - " ASN A 149 " " NAG b 1 " - " ASN B 149 " " NAG c 1 " - " ASN C 149 " " NAG d 1 " - " ASN D 149 " " NAG e 1 " - " ASN E 149 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 857.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 42.6% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.653A pdb=" N LEU A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.895A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 264 Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.532A pdb=" N LEU A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 269 " --> pdb=" O THR A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 269' Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 447 removed outlier: 3.530A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'B' and resid 8 through 20 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.639A pdb=" N ALA B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.316A pdb=" N ARG B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 246 through 271 Processing helix chain 'B' and resid 279 through 309 removed outlier: 3.891A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 447 removed outlier: 3.815A pdb=" N ALA B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 424 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.717A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 246 through 268 removed outlier: 4.339A pdb=" N LEU C 268 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.573A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 446 removed outlier: 3.667A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 8 through 20 Processing helix chain 'D' and resid 70 through 73 removed outlier: 3.609A pdb=" N ALA D 73 " --> pdb=" O LYS D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.683A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 4.397A pdb=" N ARG D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 removed outlier: 3.901A pdb=" N LYS D 173 " --> pdb=" O GLY D 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 170 through 173' Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.534A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 263 removed outlier: 3.516A pdb=" N ARG D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.687A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 309 through 446 removed outlier: 3.713A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 218 through 226 removed outlier: 3.753A pdb=" N TYR E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 239 removed outlier: 3.770A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 270 removed outlier: 3.702A pdb=" N ARG E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 305 Processing helix chain 'E' and resid 309 through 446 Proline residue: E 432 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 51 removed outlier: 6.553A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 68 current: chain 'A' and resid 123 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 4.196A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 199 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR A 205 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG A 207 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER A 211 " --> pdb=" O HIS A 191 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 36 through 46 current: chain 'B' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.074A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.249A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.066A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 36 through 51 removed outlier: 6.579A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 56 through 68 current: chain 'D' and resid 123 through 135 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 98 removed outlier: 4.027A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 51 removed outlier: 9.522A pdb=" N GLY E 39 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ARG E 68 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N AASN E 41 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR E 66 " --> pdb=" O AASN E 41 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP E 43 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLN E 64 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA E 45 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N TYR E 62 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE E 47 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR E 60 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.109A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1682 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: 2.33 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4353 1.34 - 1.46: 3400 1.46 - 1.58: 6881 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14774 Sorted by residual: bond pdb=" C1 MAN d 4 " pdb=" O5 MAN d 4 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" C1 MAN a 4 " pdb=" O5 MAN a 4 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 MAN d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 MAN c 5 " pdb=" O5 MAN c 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 MAN b 5 " pdb=" O5 MAN b 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 14769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 19143 1.16 - 2.32: 723 2.32 - 3.48: 204 3.48 - 4.64: 35 4.64 - 5.80: 15 Bond angle restraints: 20120 Sorted by residual: angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 108.10 5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA TYR C 299 " pdb=" CB TYR C 299 " pdb=" CG TYR C 299 " ideal model delta sigma weight residual 113.90 108.64 5.26 1.80e+00 3.09e-01 8.53e+00 angle pdb=" N GLY D 219 " pdb=" CA GLY D 219 " pdb=" C GLY D 219 " ideal model delta sigma weight residual 112.73 116.07 -3.34 1.20e+00 6.94e-01 7.76e+00 angle pdb=" N ILE A 25 " pdb=" CA ILE A 25 " pdb=" C ILE A 25 " ideal model delta sigma weight residual 113.07 109.53 3.54 1.36e+00 5.41e-01 6.77e+00 angle pdb=" C TYR D 66 " pdb=" N TRP D 67 " pdb=" CA TRP D 67 " ideal model delta sigma weight residual 122.53 118.96 3.57 1.61e+00 3.86e-01 4.92e+00 ... (remaining 20115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 8830 21.18 - 42.36: 255 42.36 - 63.54: 35 63.54 - 84.72: 35 84.72 - 105.89: 21 Dihedral angle restraints: 9176 sinusoidal: 4156 harmonic: 5020 Sorted by residual: dihedral pdb=" O4 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C5 BMA b 3 " pdb=" O5 BMA b 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.18 105.89 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.15 105.86 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA e 3 " pdb=" C4 BMA e 3 " pdb=" C5 BMA e 3 " pdb=" O5 BMA e 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.70 105.41 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1914 0.052 - 0.105: 366 0.105 - 0.157: 72 0.157 - 0.209: 5 0.209 - 0.262: 10 Chirality restraints: 2367 Sorted by residual: chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1 NAG D 502 " pdb=" ND2 ASN D 8 " pdb=" C2 NAG D 502 " pdb=" O5 NAG D 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2364 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.022 2.00e-02 2.50e+03 1.28e-02 3.28e+00 pdb=" CG TYR A 299 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 299 " -0.016 2.00e-02 2.50e+03 9.75e-03 1.90e+00 pdb=" CG TYR C 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 299 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 299 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 299 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 299 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 299 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 299 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 143 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO D 144 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " 0.015 5.00e-02 4.00e+02 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3143 2.78 - 3.31: 13287 3.31 - 3.84: 24599 3.84 - 4.37: 29473 4.37 - 4.90: 50041 Nonbonded interactions: 120543 Sorted by model distance: nonbonded pdb=" ND2AASN A 41 " pdb=" O ARG A 169 " model vdw 2.255 3.120 nonbonded pdb=" O LEU C 259 " pdb=" OG1 THR C 262 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR C 74 " pdb=" O LEU C 79 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN E 8 " pdb=" OG SER E 10 " model vdw 2.262 3.040 nonbonded pdb=" O PHE E 435 " pdb=" ND2 ASN E 439 " model vdw 2.278 3.120 ... (remaining 120538 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 44 \ 7)) selection = (chain 'B' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 44 \ 7)) selection = (chain 'C' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 44 \ 7)) selection = (chain 'D' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 44 \ 7)) selection = (chain 'E' and (resid 4 through 40 or resid 42 through 65 or resid 67 through 44 \ 7)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.004 0.032 14819 Z= 0.176 Angle : 0.585 5.802 20250 Z= 0.288 Chirality : 0.046 0.262 2367 Planarity : 0.003 0.030 2453 Dihedral : 12.727 105.895 5947 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.39 % Allowed : 4.43 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.40 (0.22), residues: 1692 helix: 1.93 (0.22), residues: 595 sheet: 0.34 (0.25), residues: 452 loop : 0.58 (0.27), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 428 TYR 0.028 0.001 TYR A 299 PHE 0.012 0.001 PHE E 301 TRP 0.012 0.001 TRP D 67 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00356 (14774) covalent geometry : angle 0.57515 (20120) SS BOND : bond 0.00136 ( 5) SS BOND : angle 0.35958 ( 10) hydrogen bonds : bond 0.11613 ( 601) hydrogen bonds : angle 4.77480 ( 1682) link_ALPHA1-3 : bond 0.00249 ( 5) link_ALPHA1-3 : angle 1.22597 ( 15) link_ALPHA1-6 : bond 0.00322 ( 5) link_ALPHA1-6 : angle 1.18218 ( 15) link_BETA1-4 : bond 0.00474 ( 15) link_BETA1-4 : angle 1.62620 ( 45) link_NAG-ASN : bond 0.00219 ( 15) link_NAG-ASN : angle 1.57621 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 420 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9482 (tttt) cc_final: 0.8853 (ttpt) REVERT: A 55 MET cc_start: 0.8914 (mtt) cc_final: 0.8668 (mmm) REVERT: A 138 MET cc_start: 0.9046 (mtt) cc_final: 0.8708 (mtt) REVERT: B 95 ASP cc_start: 0.8484 (p0) cc_final: 0.8185 (p0) REVERT: B 153 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8263 (mm-30) REVERT: C 40 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7355 (mpt) REVERT: C 286 MET cc_start: 0.8402 (ttm) cc_final: 0.8023 (ttp) REVERT: D 13 LYS cc_start: 0.8925 (tttt) cc_final: 0.8628 (tttm) REVERT: D 55 MET cc_start: 0.8910 (mtt) cc_final: 0.8623 (mtp) REVERT: D 153 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7989 (mm-30) REVERT: D 266 THR cc_start: 0.7970 (m) cc_final: 0.7482 (p) REVERT: D 274 LYS cc_start: 0.8626 (mttt) cc_final: 0.8371 (mmmm) REVERT: D 301 PHE cc_start: 0.8196 (t80) cc_final: 0.7886 (t80) REVERT: D 425 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8182 (mmm160) REVERT: E 13 LYS cc_start: 0.9085 (tttt) cc_final: 0.8806 (tttp) REVERT: E 155 GLU cc_start: 0.8608 (tt0) cc_final: 0.8362 (tt0) REVERT: E 190 GLU cc_start: 0.8385 (tt0) cc_final: 0.8061 (tt0) REVERT: E 215 LYS cc_start: 0.8719 (tttt) cc_final: 0.8280 (tttt) outliers start: 21 outliers final: 15 residues processed: 432 average time/residue: 0.1321 time to fit residues: 81.0619 Evaluate side-chains 339 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 323 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN B 41 ASN A B 185 GLN B 224 GLN B 265 ASN C 41 ASN A C 41 ASN B D 185 GLN D 224 GLN D 303 ASN E 41 ASN A E 185 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.083420 restraints weight = 67012.759| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.50 r_work: 0.2821 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14819 Z= 0.125 Angle : 0.576 9.107 20250 Z= 0.291 Chirality : 0.045 0.216 2367 Planarity : 0.004 0.033 2453 Dihedral : 10.896 82.683 2764 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.98 % Allowed : 11.31 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.35 (0.21), residues: 1692 helix: 1.69 (0.21), residues: 595 sheet: 0.40 (0.25), residues: 452 loop : 0.71 (0.27), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 180 TYR 0.028 0.002 TYR C 244 PHE 0.017 0.001 PHE A 289 TRP 0.013 0.001 TRP C 237 HIS 0.011 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00268 (14774) covalent geometry : angle 0.56129 (20120) SS BOND : bond 0.00732 ( 5) SS BOND : angle 1.34843 ( 10) hydrogen bonds : bond 0.04178 ( 601) hydrogen bonds : angle 4.42511 ( 1682) link_ALPHA1-3 : bond 0.00857 ( 5) link_ALPHA1-3 : angle 2.08062 ( 15) link_ALPHA1-6 : bond 0.00600 ( 5) link_ALPHA1-6 : angle 1.86052 ( 15) link_BETA1-4 : bond 0.00428 ( 15) link_BETA1-4 : angle 1.53139 ( 45) link_NAG-ASN : bond 0.00298 ( 15) link_NAG-ASN : angle 1.69245 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 351 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9340 (tttt) cc_final: 0.8519 (ttpt) REVERT: A 17 ASP cc_start: 0.9175 (m-30) cc_final: 0.8698 (m-30) REVERT: A 55 MET cc_start: 0.9012 (mtt) cc_final: 0.8379 (mmm) REVERT: A 163 ASP cc_start: 0.8848 (m-30) cc_final: 0.8423 (m-30) REVERT: B 18 LYS cc_start: 0.8866 (tttt) cc_final: 0.8448 (tmtt) REVERT: B 95 ASP cc_start: 0.8587 (p0) cc_final: 0.8039 (p0) REVERT: B 298 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8857 (tm-30) REVERT: B 425 ARG cc_start: 0.8100 (ptt180) cc_final: 0.7757 (ptm160) REVERT: C 147 GLU cc_start: 0.9016 (tt0) cc_final: 0.8796 (tt0) REVERT: C 215 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8658 (ttmm) REVERT: C 243 ASN cc_start: 0.7908 (t0) cc_final: 0.7563 (t0) REVERT: C 244 TYR cc_start: 0.8247 (p90) cc_final: 0.8006 (p90) REVERT: C 267 HIS cc_start: 0.7053 (t70) cc_final: 0.6818 (t70) REVERT: C 286 MET cc_start: 0.8364 (ttm) cc_final: 0.7893 (ttp) REVERT: D 13 LYS cc_start: 0.8684 (tttt) cc_final: 0.8438 (tttm) REVERT: D 30 ASP cc_start: 0.8899 (m-30) cc_final: 0.8523 (t0) REVERT: D 52 GLU cc_start: 0.8672 (mp0) cc_final: 0.8039 (mp0) REVERT: D 153 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8140 (mm-30) REVERT: D 182 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8053 (mt-10) REVERT: D 274 LYS cc_start: 0.8630 (mttt) cc_final: 0.8269 (mmmm) REVERT: D 301 PHE cc_start: 0.8343 (t80) cc_final: 0.8006 (t80) REVERT: D 312 ARG cc_start: 0.7746 (tpp-160) cc_final: 0.7438 (tpp80) REVERT: D 425 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8204 (mtp-110) REVERT: E 13 LYS cc_start: 0.8689 (tttt) cc_final: 0.8365 (tttp) REVERT: E 17 ASP cc_start: 0.8547 (m-30) cc_final: 0.8341 (m-30) REVERT: E 153 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8152 (mm-30) REVERT: E 155 GLU cc_start: 0.8949 (tt0) cc_final: 0.8518 (tt0) REVERT: E 180 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7301 (mtm-85) REVERT: E 215 LYS cc_start: 0.8464 (tttt) cc_final: 0.7868 (tttt) REVERT: E 227 MET cc_start: 0.8090 (ttm) cc_final: 0.7800 (ttp) outliers start: 30 outliers final: 21 residues processed: 372 average time/residue: 0.1343 time to fit residues: 71.3237 Evaluate side-chains 341 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 320 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.081311 restraints weight = 53822.730| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.09 r_work: 0.2803 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14819 Z= 0.181 Angle : 0.584 7.989 20250 Z= 0.295 Chirality : 0.046 0.221 2367 Planarity : 0.004 0.036 2453 Dihedral : 10.417 77.733 2754 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.38 % Allowed : 12.24 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.23 (0.21), residues: 1692 helix: 1.55 (0.21), residues: 595 sheet: 0.50 (0.25), residues: 442 loop : 0.53 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 192 TYR 0.033 0.002 TYR A 299 PHE 0.014 0.001 PHE E 289 TRP 0.012 0.001 TRP C 237 HIS 0.007 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00419 (14774) covalent geometry : angle 0.57011 (20120) SS BOND : bond 0.00207 ( 5) SS BOND : angle 1.41381 ( 10) hydrogen bonds : bond 0.04212 ( 601) hydrogen bonds : angle 4.49868 ( 1682) link_ALPHA1-3 : bond 0.00880 ( 5) link_ALPHA1-3 : angle 2.05077 ( 15) link_ALPHA1-6 : bond 0.00673 ( 5) link_ALPHA1-6 : angle 2.01408 ( 15) link_BETA1-4 : bond 0.00287 ( 15) link_BETA1-4 : angle 1.58803 ( 45) link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 1.59685 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 326 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9316 (tttt) cc_final: 0.8545 (ttpt) REVERT: A 17 ASP cc_start: 0.9154 (m-30) cc_final: 0.8651 (m-30) REVERT: A 55 MET cc_start: 0.9029 (mtt) cc_final: 0.8460 (mmm) REVERT: A 229 SER cc_start: 0.9080 (m) cc_final: 0.8630 (t) REVERT: B 18 LYS cc_start: 0.8934 (tttt) cc_final: 0.8477 (tmtt) REVERT: B 95 ASP cc_start: 0.8605 (p0) cc_final: 0.8104 (p0) REVERT: B 425 ARG cc_start: 0.8127 (ptt180) cc_final: 0.7864 (ptm160) REVERT: C 14 GLU cc_start: 0.8771 (pt0) cc_final: 0.8204 (pt0) REVERT: C 123 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8969 (m) REVERT: C 147 GLU cc_start: 0.9009 (tt0) cc_final: 0.8784 (tt0) REVERT: C 215 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8640 (ttmt) REVERT: C 227 MET cc_start: 0.8857 (tmm) cc_final: 0.8624 (tmm) REVERT: C 243 ASN cc_start: 0.7954 (t0) cc_final: 0.7709 (t0) REVERT: C 267 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6819 (t70) REVERT: C 286 MET cc_start: 0.8377 (ttm) cc_final: 0.8018 (ttt) REVERT: D 13 LYS cc_start: 0.8703 (tttt) cc_final: 0.8453 (tttm) REVERT: D 30 ASP cc_start: 0.8844 (m-30) cc_final: 0.8498 (t0) REVERT: D 52 GLU cc_start: 0.8615 (mp0) cc_final: 0.7834 (mp0) REVERT: D 153 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8020 (mm-30) REVERT: D 182 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8061 (mt-10) REVERT: D 274 LYS cc_start: 0.8638 (mttt) cc_final: 0.8284 (mmmm) REVERT: D 301 PHE cc_start: 0.8224 (t80) cc_final: 0.7928 (t80) REVERT: D 312 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7490 (tpp80) REVERT: D 425 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8140 (mtp-110) REVERT: E 13 LYS cc_start: 0.8756 (tttt) cc_final: 0.8541 (tttp) REVERT: E 17 ASP cc_start: 0.8521 (m-30) cc_final: 0.8313 (m-30) REVERT: E 153 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8680 (mm-30) REVERT: E 155 GLU cc_start: 0.8931 (tt0) cc_final: 0.8525 (tt0) REVERT: E 180 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7318 (mtm-85) REVERT: E 192 ARG cc_start: 0.8689 (mtm-85) cc_final: 0.8480 (ttm-80) REVERT: E 215 LYS cc_start: 0.8473 (tttt) cc_final: 0.7903 (tttt) REVERT: E 227 MET cc_start: 0.8081 (ttm) cc_final: 0.7799 (ttp) outliers start: 36 outliers final: 27 residues processed: 344 average time/residue: 0.1321 time to fit residues: 64.9334 Evaluate side-chains 339 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 310 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 267 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 50 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN A ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.082650 restraints weight = 56820.382| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.21 r_work: 0.2825 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14819 Z= 0.123 Angle : 0.555 8.425 20250 Z= 0.277 Chirality : 0.046 0.234 2367 Planarity : 0.003 0.039 2453 Dihedral : 9.606 71.042 2754 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.98 % Allowed : 12.37 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.29 (0.21), residues: 1692 helix: 1.59 (0.22), residues: 595 sheet: 0.55 (0.25), residues: 437 loop : 0.57 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 180 TYR 0.034 0.001 TYR A 299 PHE 0.013 0.001 PHE B 301 TRP 0.017 0.001 TRP C 237 HIS 0.006 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00273 (14774) covalent geometry : angle 0.54223 (20120) SS BOND : bond 0.00165 ( 5) SS BOND : angle 0.97314 ( 10) hydrogen bonds : bond 0.03884 ( 601) hydrogen bonds : angle 4.39352 ( 1682) link_ALPHA1-3 : bond 0.01014 ( 5) link_ALPHA1-3 : angle 2.12908 ( 15) link_ALPHA1-6 : bond 0.00868 ( 5) link_ALPHA1-6 : angle 2.00420 ( 15) link_BETA1-4 : bond 0.00303 ( 15) link_BETA1-4 : angle 1.42136 ( 45) link_NAG-ASN : bond 0.00206 ( 15) link_NAG-ASN : angle 1.42597 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9316 (tttt) cc_final: 0.8524 (ttpt) REVERT: A 17 ASP cc_start: 0.9090 (m-30) cc_final: 0.8496 (m-30) REVERT: A 55 MET cc_start: 0.9025 (mtt) cc_final: 0.8414 (mmm) REVERT: A 301 PHE cc_start: 0.8813 (t80) cc_final: 0.8410 (t80) REVERT: B 18 LYS cc_start: 0.8934 (tttt) cc_final: 0.8473 (tmtt) REVERT: B 52 GLU cc_start: 0.8186 (mp0) cc_final: 0.7941 (mp0) REVERT: B 95 ASP cc_start: 0.8579 (p0) cc_final: 0.8069 (p0) REVERT: B 425 ARG cc_start: 0.8160 (ptt180) cc_final: 0.7906 (ptm160) REVERT: C 14 GLU cc_start: 0.8792 (pt0) cc_final: 0.8228 (pt0) REVERT: C 17 ASP cc_start: 0.8810 (m-30) cc_final: 0.8410 (m-30) REVERT: C 70 LYS cc_start: 0.9234 (mmtm) cc_final: 0.9001 (mmtm) REVERT: C 123 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8931 (m) REVERT: C 147 GLU cc_start: 0.8979 (tt0) cc_final: 0.8736 (tt0) REVERT: C 215 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8628 (ttmt) REVERT: C 227 MET cc_start: 0.8872 (tmm) cc_final: 0.8613 (tmm) REVERT: C 243 ASN cc_start: 0.7969 (t0) cc_final: 0.7639 (t0) REVERT: C 244 TYR cc_start: 0.8177 (p90) cc_final: 0.7961 (p90) REVERT: C 267 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6877 (t70) REVERT: C 286 MET cc_start: 0.8329 (ttm) cc_final: 0.7595 (ttp) REVERT: D 13 LYS cc_start: 0.8712 (tttt) cc_final: 0.8507 (tttp) REVERT: D 30 ASP cc_start: 0.8843 (m-30) cc_final: 0.8421 (t0) REVERT: D 52 GLU cc_start: 0.8597 (mp0) cc_final: 0.7937 (mp0) REVERT: D 153 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8027 (mm-30) REVERT: D 182 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8060 (mt-10) REVERT: D 274 LYS cc_start: 0.8571 (mttt) cc_final: 0.8224 (mmmm) REVERT: D 301 PHE cc_start: 0.8275 (t80) cc_final: 0.7990 (t80) REVERT: D 312 ARG cc_start: 0.7724 (tpp-160) cc_final: 0.7481 (tpp80) REVERT: D 425 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.8135 (mtp-110) REVERT: E 17 ASP cc_start: 0.8560 (m-30) cc_final: 0.8354 (m-30) REVERT: E 180 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: E 215 LYS cc_start: 0.8419 (tttt) cc_final: 0.7899 (tttt) REVERT: E 227 MET cc_start: 0.8108 (ttm) cc_final: 0.7850 (ttp) outliers start: 44 outliers final: 26 residues processed: 339 average time/residue: 0.1276 time to fit residues: 62.1552 Evaluate side-chains 318 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 148 GLN D 185 GLN E 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081253 restraints weight = 63935.873| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.44 r_work: 0.2795 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14819 Z= 0.156 Angle : 0.573 8.250 20250 Z= 0.285 Chirality : 0.046 0.245 2367 Planarity : 0.004 0.043 2453 Dihedral : 9.283 68.374 2754 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.65 % Allowed : 13.16 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.29 (0.21), residues: 1692 helix: 1.61 (0.22), residues: 595 sheet: 0.56 (0.24), residues: 442 loop : 0.55 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 180 TYR 0.031 0.002 TYR A 299 PHE 0.022 0.001 PHE B 306 TRP 0.016 0.001 TRP C 237 HIS 0.006 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00361 (14774) covalent geometry : angle 0.55948 (20120) SS BOND : bond 0.00178 ( 5) SS BOND : angle 1.15712 ( 10) hydrogen bonds : bond 0.03933 ( 601) hydrogen bonds : angle 4.41851 ( 1682) link_ALPHA1-3 : bond 0.00988 ( 5) link_ALPHA1-3 : angle 2.23853 ( 15) link_ALPHA1-6 : bond 0.00857 ( 5) link_ALPHA1-6 : angle 2.05677 ( 15) link_BETA1-4 : bond 0.00300 ( 15) link_BETA1-4 : angle 1.47855 ( 45) link_NAG-ASN : bond 0.00157 ( 15) link_NAG-ASN : angle 1.44165 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 294 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9315 (tttt) cc_final: 0.8526 (ttpt) REVERT: A 17 ASP cc_start: 0.9102 (m-30) cc_final: 0.8525 (m-30) REVERT: A 55 MET cc_start: 0.9066 (mtt) cc_final: 0.8423 (mmm) REVERT: A 224 GLN cc_start: 0.8975 (tp40) cc_final: 0.8707 (tp40) REVERT: A 299 TYR cc_start: 0.8297 (t80) cc_final: 0.7741 (t80) REVERT: B 18 LYS cc_start: 0.8939 (tttt) cc_final: 0.8483 (tmtt) REVERT: B 95 ASP cc_start: 0.8691 (p0) cc_final: 0.8206 (p0) REVERT: B 425 ARG cc_start: 0.8128 (ptt180) cc_final: 0.7885 (ptm160) REVERT: C 14 GLU cc_start: 0.8814 (pt0) cc_final: 0.8217 (pt0) REVERT: C 40 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.7298 (mpt) REVERT: C 123 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8918 (m) REVERT: C 215 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8636 (ttmt) REVERT: C 227 MET cc_start: 0.8889 (tmm) cc_final: 0.8627 (tmm) REVERT: C 243 ASN cc_start: 0.7973 (t0) cc_final: 0.7623 (t0) REVERT: C 267 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6814 (t70) REVERT: C 286 MET cc_start: 0.8335 (ttm) cc_final: 0.7680 (ttp) REVERT: D 21 LYS cc_start: 0.8798 (tppp) cc_final: 0.8596 (tppt) REVERT: D 30 ASP cc_start: 0.8858 (m-30) cc_final: 0.8430 (t0) REVERT: D 52 GLU cc_start: 0.8577 (mp0) cc_final: 0.7990 (mp0) REVERT: D 153 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 182 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7892 (tp30) REVERT: D 274 LYS cc_start: 0.8573 (mttt) cc_final: 0.8265 (mmmm) REVERT: D 312 ARG cc_start: 0.7751 (tpp-160) cc_final: 0.7516 (tpp80) REVERT: D 425 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8091 (mtp180) REVERT: E 227 MET cc_start: 0.8108 (ttm) cc_final: 0.7865 (ttp) outliers start: 39 outliers final: 31 residues processed: 314 average time/residue: 0.1239 time to fit residues: 56.1009 Evaluate side-chains 323 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 289 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.082113 restraints weight = 59540.405| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.19 r_work: 0.2824 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14819 Z= 0.131 Angle : 0.569 9.749 20250 Z= 0.284 Chirality : 0.046 0.250 2367 Planarity : 0.004 0.054 2453 Dihedral : 8.886 65.221 2754 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.71 % Allowed : 13.49 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.33 (0.21), residues: 1692 helix: 1.67 (0.22), residues: 590 sheet: 0.59 (0.24), residues: 442 loop : 0.54 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 180 TYR 0.029 0.001 TYR A 299 PHE 0.019 0.001 PHE A 289 TRP 0.019 0.001 TRP C 237 HIS 0.006 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00299 (14774) covalent geometry : angle 0.55655 (20120) SS BOND : bond 0.00164 ( 5) SS BOND : angle 0.98752 ( 10) hydrogen bonds : bond 0.03819 ( 601) hydrogen bonds : angle 4.40539 ( 1682) link_ALPHA1-3 : bond 0.01026 ( 5) link_ALPHA1-3 : angle 2.23712 ( 15) link_ALPHA1-6 : bond 0.00938 ( 5) link_ALPHA1-6 : angle 2.01419 ( 15) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.40791 ( 45) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 1.39223 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9343 (tttt) cc_final: 0.8518 (ttpt) REVERT: A 17 ASP cc_start: 0.9071 (m-30) cc_final: 0.8484 (m-30) REVERT: A 55 MET cc_start: 0.9023 (mtt) cc_final: 0.8415 (mmm) REVERT: A 224 GLN cc_start: 0.8959 (tp40) cc_final: 0.8701 (tp40) REVERT: A 227 MET cc_start: 0.8185 (mmt) cc_final: 0.7863 (mmt) REVERT: A 299 TYR cc_start: 0.8171 (t80) cc_final: 0.7651 (t80) REVERT: B 18 LYS cc_start: 0.8948 (tttt) cc_final: 0.8506 (tmtt) REVERT: B 95 ASP cc_start: 0.8572 (p0) cc_final: 0.8060 (p0) REVERT: B 425 ARG cc_start: 0.8144 (ptt180) cc_final: 0.7901 (ptm160) REVERT: C 14 GLU cc_start: 0.8851 (pt0) cc_final: 0.8262 (pt0) REVERT: C 123 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8897 (m) REVERT: C 227 MET cc_start: 0.8858 (tmm) cc_final: 0.8642 (tmm) REVERT: C 243 ASN cc_start: 0.8035 (t0) cc_final: 0.7748 (t0) REVERT: C 267 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6842 (t70) REVERT: C 286 MET cc_start: 0.8315 (ttm) cc_final: 0.7680 (ttp) REVERT: D 30 ASP cc_start: 0.8811 (m-30) cc_final: 0.8472 (t0) REVERT: D 153 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8047 (mm-30) REVERT: D 274 LYS cc_start: 0.8647 (mttt) cc_final: 0.8226 (mmmm) REVERT: D 425 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8099 (mtp-110) REVERT: E 180 ARG cc_start: 0.7539 (mtm110) cc_final: 0.7273 (mtm-85) REVERT: E 220 TYR cc_start: 0.8546 (t80) cc_final: 0.8339 (t80) REVERT: E 227 MET cc_start: 0.8079 (ttm) cc_final: 0.7810 (ttp) outliers start: 40 outliers final: 30 residues processed: 319 average time/residue: 0.1244 time to fit residues: 58.2325 Evaluate side-chains 334 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.0000 chunk 98 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083457 restraints weight = 59461.286| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.17 r_work: 0.2845 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14819 Z= 0.116 Angle : 0.568 9.535 20250 Z= 0.282 Chirality : 0.046 0.253 2367 Planarity : 0.003 0.048 2453 Dihedral : 8.431 61.543 2754 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.38 % Allowed : 14.29 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.39 (0.21), residues: 1692 helix: 1.69 (0.22), residues: 590 sheet: 0.65 (0.24), residues: 442 loop : 0.57 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 180 TYR 0.027 0.001 TYR E 445 PHE 0.015 0.001 PHE C 306 TRP 0.024 0.001 TRP C 237 HIS 0.008 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00261 (14774) covalent geometry : angle 0.55677 (20120) SS BOND : bond 0.00152 ( 5) SS BOND : angle 0.82826 ( 10) hydrogen bonds : bond 0.03643 ( 601) hydrogen bonds : angle 4.36005 ( 1682) link_ALPHA1-3 : bond 0.01065 ( 5) link_ALPHA1-3 : angle 2.19761 ( 15) link_ALPHA1-6 : bond 0.01018 ( 5) link_ALPHA1-6 : angle 1.94519 ( 15) link_BETA1-4 : bond 0.00364 ( 15) link_BETA1-4 : angle 1.32629 ( 45) link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.34200 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 324 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9371 (tttt) cc_final: 0.8489 (ttpt) REVERT: A 17 ASP cc_start: 0.9040 (m-30) cc_final: 0.8462 (m-30) REVERT: A 55 MET cc_start: 0.9014 (mtt) cc_final: 0.8408 (mmm) REVERT: A 163 ASP cc_start: 0.8935 (m-30) cc_final: 0.8627 (t0) REVERT: A 224 GLN cc_start: 0.8876 (tp40) cc_final: 0.8629 (tp40) REVERT: B 18 LYS cc_start: 0.8948 (tttt) cc_final: 0.8498 (tmtt) REVERT: B 95 ASP cc_start: 0.8588 (p0) cc_final: 0.8070 (p0) REVERT: B 173 LYS cc_start: 0.9262 (mttt) cc_final: 0.8833 (mmmt) REVERT: B 425 ARG cc_start: 0.8232 (ptt180) cc_final: 0.8003 (ptm160) REVERT: C 14 GLU cc_start: 0.8843 (pt0) cc_final: 0.8337 (pt0) REVERT: C 40 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.7288 (mpt) REVERT: C 123 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8851 (m) REVERT: C 215 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8595 (ttmm) REVERT: C 243 ASN cc_start: 0.8119 (t0) cc_final: 0.7783 (t0) REVERT: C 275 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7892 (pt) REVERT: C 286 MET cc_start: 0.8260 (ttm) cc_final: 0.7653 (ttp) REVERT: C 425 ARG cc_start: 0.8342 (ppt170) cc_final: 0.7979 (ptt90) REVERT: D 30 ASP cc_start: 0.8817 (m-30) cc_final: 0.8493 (t0) REVERT: D 52 GLU cc_start: 0.8476 (mp0) cc_final: 0.7879 (mp0) REVERT: D 95 ASP cc_start: 0.8897 (p0) cc_final: 0.8342 (p0) REVERT: D 153 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8060 (mm-30) REVERT: D 274 LYS cc_start: 0.8684 (mttt) cc_final: 0.8288 (mmmm) REVERT: D 425 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8039 (mtp180) REVERT: E 55 MET cc_start: 0.8958 (mmm) cc_final: 0.8737 (mmt) REVERT: E 153 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8655 (mm-30) REVERT: E 155 GLU cc_start: 0.8884 (tt0) cc_final: 0.8524 (tt0) REVERT: E 180 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7295 (mtm-85) REVERT: E 227 MET cc_start: 0.8054 (ttm) cc_final: 0.7783 (ttp) outliers start: 35 outliers final: 30 residues processed: 341 average time/residue: 0.1246 time to fit residues: 62.0987 Evaluate side-chains 341 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.081232 restraints weight = 74138.882| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.57 r_work: 0.2807 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14819 Z= 0.143 Angle : 0.584 9.520 20250 Z= 0.289 Chirality : 0.046 0.256 2367 Planarity : 0.004 0.055 2453 Dihedral : 8.168 59.749 2754 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.65 % Allowed : 14.42 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.31 (0.21), residues: 1692 helix: 1.59 (0.21), residues: 590 sheet: 0.65 (0.24), residues: 442 loop : 0.54 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 180 TYR 0.040 0.001 TYR A 299 PHE 0.021 0.001 PHE A 289 TRP 0.024 0.001 TRP C 237 HIS 0.007 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00329 (14774) covalent geometry : angle 0.57177 (20120) SS BOND : bond 0.00173 ( 5) SS BOND : angle 1.05186 ( 10) hydrogen bonds : bond 0.03751 ( 601) hydrogen bonds : angle 4.38960 ( 1682) link_ALPHA1-3 : bond 0.01015 ( 5) link_ALPHA1-3 : angle 2.28250 ( 15) link_ALPHA1-6 : bond 0.01003 ( 5) link_ALPHA1-6 : angle 1.93598 ( 15) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.41676 ( 45) link_NAG-ASN : bond 0.00166 ( 15) link_NAG-ASN : angle 1.37058 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9375 (tttt) cc_final: 0.8507 (ttpt) REVERT: A 17 ASP cc_start: 0.9055 (m-30) cc_final: 0.8460 (m-30) REVERT: A 55 MET cc_start: 0.9058 (mtt) cc_final: 0.8440 (mmm) REVERT: A 163 ASP cc_start: 0.8998 (m-30) cc_final: 0.8660 (t0) REVERT: A 224 GLN cc_start: 0.8930 (tp40) cc_final: 0.8720 (tp40) REVERT: A 227 MET cc_start: 0.8355 (mmt) cc_final: 0.8080 (mmt) REVERT: B 18 LYS cc_start: 0.8963 (tttt) cc_final: 0.8509 (tmtt) REVERT: B 95 ASP cc_start: 0.8644 (p0) cc_final: 0.8164 (p0) REVERT: B 173 LYS cc_start: 0.9270 (mttt) cc_final: 0.8836 (mmmt) REVERT: B 425 ARG cc_start: 0.8169 (ptt180) cc_final: 0.7946 (ptm160) REVERT: C 40 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.7306 (mpt) REVERT: C 123 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8886 (m) REVERT: C 215 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8748 (ttmt) REVERT: C 243 ASN cc_start: 0.8065 (t0) cc_final: 0.7706 (t0) REVERT: C 275 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7684 (pt) REVERT: C 286 MET cc_start: 0.8297 (ttm) cc_final: 0.7680 (ttp) REVERT: C 425 ARG cc_start: 0.8376 (ppt170) cc_final: 0.8092 (ptt90) REVERT: D 30 ASP cc_start: 0.8839 (m-30) cc_final: 0.8496 (t0) REVERT: D 52 GLU cc_start: 0.8532 (mp0) cc_final: 0.7762 (mp0) REVERT: D 95 ASP cc_start: 0.8952 (p0) cc_final: 0.8398 (p0) REVERT: D 153 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8071 (mm-30) REVERT: D 274 LYS cc_start: 0.8677 (mttt) cc_final: 0.8285 (mmmm) REVERT: D 425 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8030 (mtp-110) REVERT: E 153 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8704 (mm-30) REVERT: E 155 GLU cc_start: 0.8933 (tt0) cc_final: 0.8576 (tt0) REVERT: E 172 ASP cc_start: 0.8613 (m-30) cc_final: 0.8218 (p0) REVERT: E 180 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7223 (mtm-85) outliers start: 39 outliers final: 31 residues processed: 330 average time/residue: 0.1213 time to fit residues: 58.5562 Evaluate side-chains 333 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 1.9990 chunk 159 optimal weight: 0.0020 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 34 optimal weight: 0.0050 chunk 75 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.082926 restraints weight = 56354.531| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.07 r_work: 0.2839 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14819 Z= 0.133 Angle : 0.581 9.921 20250 Z= 0.288 Chirality : 0.046 0.250 2367 Planarity : 0.003 0.037 2453 Dihedral : 7.899 57.528 2754 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.51 % Allowed : 14.62 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.33 (0.21), residues: 1692 helix: 1.60 (0.22), residues: 590 sheet: 0.66 (0.24), residues: 442 loop : 0.55 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 180 TYR 0.041 0.001 TYR A 299 PHE 0.028 0.001 PHE B 306 TRP 0.024 0.001 TRP C 237 HIS 0.008 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00306 (14774) covalent geometry : angle 0.57010 (20120) SS BOND : bond 0.00177 ( 5) SS BOND : angle 0.95471 ( 10) hydrogen bonds : bond 0.03699 ( 601) hydrogen bonds : angle 4.38355 ( 1682) link_ALPHA1-3 : bond 0.00993 ( 5) link_ALPHA1-3 : angle 2.23387 ( 15) link_ALPHA1-6 : bond 0.01021 ( 5) link_ALPHA1-6 : angle 1.82659 ( 15) link_BETA1-4 : bond 0.00365 ( 15) link_BETA1-4 : angle 1.38565 ( 45) link_NAG-ASN : bond 0.00179 ( 15) link_NAG-ASN : angle 1.34918 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9385 (tttt) cc_final: 0.8501 (ttpt) REVERT: A 17 ASP cc_start: 0.9046 (m-30) cc_final: 0.8447 (m-30) REVERT: A 55 MET cc_start: 0.8996 (mtt) cc_final: 0.8360 (mmm) REVERT: A 163 ASP cc_start: 0.8958 (m-30) cc_final: 0.8636 (t0) REVERT: A 224 GLN cc_start: 0.8876 (tp40) cc_final: 0.8675 (tp40) REVERT: A 227 MET cc_start: 0.8311 (mmt) cc_final: 0.7999 (mmt) REVERT: B 18 LYS cc_start: 0.8958 (tttt) cc_final: 0.8516 (tmtt) REVERT: B 95 ASP cc_start: 0.8631 (p0) cc_final: 0.8158 (p0) REVERT: B 173 LYS cc_start: 0.9281 (mttt) cc_final: 0.8819 (mmmt) REVERT: B 425 ARG cc_start: 0.8154 (ptt180) cc_final: 0.7940 (ptm160) REVERT: C 40 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.7276 (mpt) REVERT: C 123 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8848 (m) REVERT: C 215 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8693 (tppt) REVERT: C 243 ASN cc_start: 0.8040 (t0) cc_final: 0.7715 (t0) REVERT: C 275 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7678 (pt) REVERT: C 286 MET cc_start: 0.8241 (ttm) cc_final: 0.7636 (ttp) REVERT: C 425 ARG cc_start: 0.8334 (ppt170) cc_final: 0.8042 (ptt90) REVERT: D 30 ASP cc_start: 0.8802 (m-30) cc_final: 0.8493 (t0) REVERT: D 52 GLU cc_start: 0.8572 (mp0) cc_final: 0.7825 (mp0) REVERT: D 95 ASP cc_start: 0.8906 (p0) cc_final: 0.8372 (p0) REVERT: D 153 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8032 (mm-30) REVERT: D 182 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7961 (tp30) REVERT: D 274 LYS cc_start: 0.8691 (mttt) cc_final: 0.8302 (mmmm) REVERT: D 425 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8029 (mtp-110) REVERT: E 153 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8633 (mm-30) REVERT: E 155 GLU cc_start: 0.8886 (tt0) cc_final: 0.8526 (tt0) REVERT: E 172 ASP cc_start: 0.8575 (m-30) cc_final: 0.8218 (p0) REVERT: E 180 ARG cc_start: 0.7485 (mtm110) cc_final: 0.7221 (mtm-85) outliers start: 37 outliers final: 31 residues processed: 326 average time/residue: 0.1200 time to fit residues: 57.4268 Evaluate side-chains 326 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 128 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 94 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B B 224 GLN E 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.084475 restraints weight = 69085.277| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.60 r_work: 0.2839 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14819 Z= 0.110 Angle : 0.563 9.591 20250 Z= 0.279 Chirality : 0.045 0.234 2367 Planarity : 0.004 0.054 2453 Dihedral : 7.446 58.909 2754 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.18 % Allowed : 15.01 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.38 (0.21), residues: 1692 helix: 1.60 (0.22), residues: 590 sheet: 0.74 (0.25), residues: 442 loop : 0.60 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 180 TYR 0.038 0.001 TYR A 299 PHE 0.028 0.001 PHE B 306 TRP 0.030 0.001 TRP C 237 HIS 0.007 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00244 (14774) covalent geometry : angle 0.55339 (20120) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.75140 ( 10) hydrogen bonds : bond 0.03510 ( 601) hydrogen bonds : angle 4.33133 ( 1682) link_ALPHA1-3 : bond 0.01029 ( 5) link_ALPHA1-3 : angle 2.10208 ( 15) link_ALPHA1-6 : bond 0.01083 ( 5) link_ALPHA1-6 : angle 1.53031 ( 15) link_BETA1-4 : bond 0.00444 ( 15) link_BETA1-4 : angle 1.32545 ( 45) link_NAG-ASN : bond 0.00224 ( 15) link_NAG-ASN : angle 1.26822 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9351 (tttt) cc_final: 0.8400 (ttmt) REVERT: A 17 ASP cc_start: 0.9013 (m-30) cc_final: 0.8417 (m-30) REVERT: A 55 MET cc_start: 0.9000 (mtt) cc_final: 0.8341 (mmm) REVERT: A 90 GLN cc_start: 0.8433 (mp10) cc_final: 0.7874 (mp10) REVERT: A 163 ASP cc_start: 0.8965 (m-30) cc_final: 0.8652 (t0) REVERT: A 224 GLN cc_start: 0.8857 (tp40) cc_final: 0.8655 (tp40) REVERT: A 227 MET cc_start: 0.8255 (mmt) cc_final: 0.7947 (mmt) REVERT: B 18 LYS cc_start: 0.8938 (tttt) cc_final: 0.8484 (tmtt) REVERT: B 95 ASP cc_start: 0.8642 (p0) cc_final: 0.8160 (p0) REVERT: B 173 LYS cc_start: 0.9267 (mttt) cc_final: 0.8800 (mmmt) REVERT: B 425 ARG cc_start: 0.8156 (ptt180) cc_final: 0.7938 (ptm160) REVERT: C 9 MET cc_start: 0.8435 (mmt) cc_final: 0.8188 (mmt) REVERT: C 17 ASP cc_start: 0.8709 (m-30) cc_final: 0.8424 (m-30) REVERT: C 40 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.7257 (mpt) REVERT: C 123 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8853 (m) REVERT: C 243 ASN cc_start: 0.8064 (t0) cc_final: 0.7680 (t0) REVERT: C 275 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7861 (pt) REVERT: C 286 MET cc_start: 0.8196 (ttm) cc_final: 0.7587 (ttp) REVERT: C 425 ARG cc_start: 0.8343 (ppt170) cc_final: 0.7970 (ptt90) REVERT: D 30 ASP cc_start: 0.8862 (m-30) cc_final: 0.8530 (t0) REVERT: D 52 GLU cc_start: 0.8608 (mp0) cc_final: 0.7864 (mp0) REVERT: D 95 ASP cc_start: 0.8909 (p0) cc_final: 0.8357 (p0) REVERT: D 153 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8093 (mm-30) REVERT: D 182 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7972 (tp30) REVERT: D 274 LYS cc_start: 0.8748 (mttt) cc_final: 0.8312 (mmmm) REVERT: D 425 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8049 (mtp-110) REVERT: E 155 GLU cc_start: 0.8918 (tt0) cc_final: 0.8557 (tt0) REVERT: E 180 ARG cc_start: 0.7473 (mtm110) cc_final: 0.7205 (mtm-85) REVERT: E 182 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8169 (mm-30) outliers start: 32 outliers final: 27 residues processed: 326 average time/residue: 0.1171 time to fit residues: 56.4518 Evaluate side-chains 333 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 309 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 113 optimal weight: 10.0000 chunk 145 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 156 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN D 41 ASN B E 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.084261 restraints weight = 51624.399| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.93 r_work: 0.2877 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14819 Z= 0.113 Angle : 0.572 9.603 20250 Z= 0.283 Chirality : 0.045 0.233 2367 Planarity : 0.003 0.041 2453 Dihedral : 6.908 59.758 2752 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.18 % Allowed : 15.01 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.31 % 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: 1.38 (0.21), residues: 1692 helix: 1.49 (0.22), residues: 595 sheet: 0.63 (0.25), residues: 452 loop : 0.80 (0.27), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 180 TYR 0.036 0.001 TYR A 299 PHE 0.024 0.001 PHE A 301 TRP 0.032 0.001 TRP C 237 HIS 0.007 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00251 (14774) covalent geometry : angle 0.56264 (20120) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.79790 ( 10) hydrogen bonds : bond 0.03476 ( 601) hydrogen bonds : angle 4.30915 ( 1682) link_ALPHA1-3 : bond 0.00993 ( 5) link_ALPHA1-3 : angle 2.04924 ( 15) link_ALPHA1-6 : bond 0.01102 ( 5) link_ALPHA1-6 : angle 1.31972 ( 15) link_BETA1-4 : bond 0.00461 ( 15) link_BETA1-4 : angle 1.35743 ( 45) link_NAG-ASN : bond 0.00221 ( 15) link_NAG-ASN : angle 1.26418 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3556.49 seconds wall clock time: 61 minutes 45.59 seconds (3705.59 seconds total)