Starting phenix.real_space_refine on Tue Sep 15 00:43:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yer_72860/09_2026/9yer_72860_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yer_72860/09_2026/9yer_72860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yer_72860/09_2026/9yer_72860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yer_72860/09_2026/9yer_72860.map" model { file = "/net/cci-nas-00/data/ceres_data/9yer_72860/09_2026/9yer_72860_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yer_72860/09_2026/9yer_72860_trim.cif" } resolution = 2.19 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= 0.025 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 10786 2.51 5 N 2672 2.21 5 O 3062 1.98 5 H 16384 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32979 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6376 Classifications: {'peptide': 396} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 375} Chain breaks: 2 Chain: "C" Number of atoms: 6324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6324 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 6544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6544 Classifications: {'peptide': 403} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 378} Chain breaks: 3 Chain: "D" Number of atoms: 7006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 7006 Classifications: {'peptide': 430} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 399} Chain breaks: 1 Chain: "B" Number of atoms: 6443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6443 Classifications: {'peptide': 408} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 384} Chain breaks: 1 Chain: "H" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.42, per 1000 atoms: 0.16 Number of scatterers: 32979 At special positions: 0 Unit cell: (100.045, 107.525, 164.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3062 8.00 N 2672 7.00 C 10786 6.00 H 16384 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " 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 Atom "HETATM32766 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG B 501 " - " ASN B 66 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN B 141 " " NAG J 1 " - " ASN C 141 " " NAG K 1 " - " ASN D 143 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 839.4 milliseconds 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3880 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 19 sheets defined 45.3% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.110A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.500A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 4.040A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 371 through 437 removed outlier: 4.309A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.113A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 230 through 233 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 241 through 263 Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 370 through 436 removed outlier: 4.440A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.233A pdb=" N ASP E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 275 removed outlier: 3.540A pdb=" N LYS E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.599A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 470 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.565A pdb=" N LYS D 68 " --> pdb=" O ASN D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.785A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.637A pdb=" N VAL D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 276 Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.806A pdb=" N GLU D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 473 Proline residue: D 458 - end of helix removed outlier: 3.518A pdb=" N GLN D 470 " --> pdb=" O TRP D 466 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.603A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.169A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.928A pdb=" N TYR B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.749A pdb=" N ALA B 241 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.710A pdb=" N GLN B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 401 through 460 removed outlier: 3.636A pdb=" N GLY B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.105A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.105A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 49 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU A 40 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A 61 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A 30 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.201A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 198 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS A 204 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.237A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.237A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ARG C 55 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE C 38 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS C 57 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLN C 36 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N GLN C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLY C 34 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL C 61 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N THR C 32 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.120A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR C 196 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR C 190 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 178 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.097A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.097A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER E 42 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU E 40 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS E 53 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR E 61 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG E 30 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.761A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.995A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.995A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.435A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.435A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 81 removed outlier: 3.677A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 81 removed outlier: 3.677A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.113A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.113A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2787 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: 7.90 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16365 1.03 - 1.23: 213 1.23 - 1.43: 6881 1.43 - 1.62: 9817 1.62 - 1.82: 119 Bond restraints: 33395 Sorted by residual: bond pdb=" NZ LYS B 69 " pdb=" HZ1 LYS B 69 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS D 15 " pdb=" HZ1 LYS D 15 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 185 " pdb=" HZ1 LYS A 185 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS A 276 " pdb=" HZ2 LYS A 276 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 57 " pdb=" HZ1 LYS C 57 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 33390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.07: 60428 13.07 - 26.13: 1 26.13 - 39.20: 1 39.20 - 52.27: 2 52.27 - 65.33: 4 Bond angle restraints: 60436 Sorted by residual: angle pdb=" CA GLU E 409 " pdb=" N GLU E 409 " pdb=" H GLU E 409 " ideal model delta sigma weight residual 114.00 179.33 -65.33 3.00e+00 1.11e-01 4.74e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 170.70 -56.70 3.00e+00 1.11e-01 3.57e+02 angle pdb=" CA VAL B 400 " pdb=" N VAL B 400 " pdb=" H VAL B 400 " ideal model delta sigma weight residual 114.00 169.00 -55.00 3.00e+00 1.11e-01 3.36e+02 angle pdb=" CA PHE D 411 " pdb=" N PHE D 411 " pdb=" H PHE D 411 " ideal model delta sigma weight residual 114.00 166.74 -52.74 3.00e+00 1.11e-01 3.09e+02 angle pdb=" CA GLY E 168 " pdb=" N GLY E 168 " pdb=" H GLY E 168 " ideal model delta sigma weight residual 114.00 162.56 -48.56 3.00e+00 1.11e-01 2.62e+02 ... (remaining 60431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 14877 21.18 - 42.35: 834 42.35 - 63.53: 254 63.53 - 84.70: 61 84.70 - 105.88: 24 Dihedral angle restraints: 16050 sinusoidal: 8854 harmonic: 7196 Sorted by residual: dihedral pdb=" CA LEU D 1 " pdb=" C LEU D 1 " pdb=" N ASN D 2 " pdb=" CA ASN D 2 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" N HIS C 25 " pdb=" C HIS C 25 " pdb=" CA HIS C 25 " pdb=" CB HIS C 25 " ideal model delta harmonic sigma weight residual 122.80 133.80 -11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" C TYR C 63 " pdb=" N TYR C 63 " pdb=" CA TYR C 63 " pdb=" CB TYR C 63 " ideal model delta harmonic sigma weight residual -122.60 -133.41 10.81 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 16047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 2747 0.328 - 0.656: 5 0.656 - 0.983: 3 0.983 - 1.311: 1 1.311 - 1.639: 1 Chirality restraints: 2757 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.19e+01 chirality pdb=" CG LEU D 111 " pdb=" CB LEU D 111 " pdb=" CD1 LEU D 111 " pdb=" CD2 LEU D 111 " both_signs ideal model delta sigma weight residual False -2.59 -0.95 -1.64 2.00e-01 2.50e+01 6.72e+01 chirality pdb=" C1 MAN K 4 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.24 0.16 2.00e-02 2.50e+03 6.67e+01 ... (remaining 2754 not shown) Planarity restraints: 4779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 141 " 0.132 2.00e-02 2.50e+03 1.62e-01 3.28e+02 pdb=" CG ASN B 141 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN B 141 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 141 " -0.271 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.185 2.00e-02 2.50e+03 1.55e-01 3.02e+02 pdb=" C7 NAG B 501 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.259 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 66 " 0.146 2.00e-02 2.50e+03 1.54e-01 2.96e+02 pdb=" CG ASN B 66 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 66 " -0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN B 66 " -0.216 2.00e-02 2.50e+03 pdb=" C1 NAG B 501 " 0.203 2.00e-02 2.50e+03 ... (remaining 4776 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 211 2.01 - 2.66: 44546 2.66 - 3.30: 99133 3.30 - 3.95: 132983 3.95 - 4.60: 202983 Nonbonded interactions: 479856 Sorted by model distance: nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.361 2.100 nonbonded pdb=" HG1 THR C 229 " pdb="HG22 VAL C 285 " model vdw 1.442 2.270 nonbonded pdb=" HZ1 LYS A 145 " pdb=" HH TYR A 190 " model vdw 1.489 2.100 nonbonded pdb=" HG SER D 105 " pdb=" H ILE D 125 " model vdw 1.500 2.100 nonbonded pdb=" HZ1 LYS B 46 " pdb=" O ALA B 271 " model vdw 1.603 2.450 ... (remaining 479851 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 1 through 324 or resid 370 through 436 or resid 501)) selection = (chain 'C' and (resid 1 through 324 or resid 370 through 501)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.260 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.005 0.200 17038 Z= 0.212 Angle : 0.786 34.369 23283 Z= 0.353 Chirality : 0.067 1.639 2757 Planarity : 0.007 0.155 2873 Dihedral : 16.956 105.879 6477 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.80 % Favored : 98.15 % Rotamer: Outliers : 0.27 % Allowed : 9.07 % Favored : 90.66 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2003 helix: 2.52 (0.17), residues: 785 sheet: -0.55 (0.25), residues: 369 loop : 0.18 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 26 TYR 0.011 0.001 TYR A 93 PHE 0.023 0.001 PHE A 284 TRP 0.010 0.001 TRP D 176 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (17011) covalent geometry : angle 0.67621 / 0.33 (23208) SS BOND : bond 0.00243 / 0.13 ( 6) SS BOND : angle 1.12059 / 0.66 ( 12) hydrogen bonds : bond 0.15083 / 10.34 ( 881) hydrogen bonds : angle 6.10772 / 4.32 ( 2787) link_ALPHA1-3 : bond 0.00392 / 0.19 ( 2) link_ALPHA1-3 : angle 2.27643 / 1.19 ( 6) link_ALPHA1-6 : bond 0.00261 / 0.13 ( 3) link_ALPHA1-6 : angle 1.69032 / 0.96 ( 9) link_BETA1-4 : bond 0.00777 / 0.58 ( 10) link_BETA1-4 : angle 3.05283 / 2.02 ( 30) link_NAG-ASN : bond 0.12249 / 6.00 ( 6) link_NAG-ASN : angle 13.80458 / 8.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 288 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7927 (tp) cc_final: 0.7542 (mm) REVERT: A 284 PHE cc_start: 0.8201 (t80) cc_final: 0.7939 (t80) REVERT: A 381 TYR cc_start: 0.8092 (t80) cc_final: 0.7815 (t80) REVERT: A 384 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6732 (mm-30) REVERT: C 410 LEU cc_start: 0.8415 (mm) cc_final: 0.8051 (mt) REVERT: E 10 LYS cc_start: 0.8436 (tttt) cc_final: 0.8167 (ttpt) REVERT: E 293 MET cc_start: 0.8279 (mtp) cc_final: 0.8069 (mtp) REVERT: E 321 LEU cc_start: 0.7801 (tp) cc_final: 0.7535 (tp) REVERT: D 73 GLU cc_start: 0.7361 (tt0) cc_final: 0.6936 (tm-30) REVERT: D 167 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7636 (ttpt) REVERT: D 276 LYS cc_start: 0.8195 (mttm) cc_final: 0.7834 (mtmt) REVERT: D 436 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 167 LYS cc_start: 0.7487 (tttp) cc_final: 0.7257 (tttm) REVERT: B 196 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7662 (mtt-85) REVERT: B 268 PHE cc_start: 0.7992 (t80) cc_final: 0.7749 (t80) REVERT: B 273 LYS cc_start: 0.7809 (tptt) cc_final: 0.7340 (mptp) REVERT: B 417 GLN cc_start: 0.7024 (mt0) cc_final: 0.6652 (mt0) outliers start: 5 outliers final: 3 residues processed: 291 average time/residue: 1.0940 time to fit residues: 361.9667 Evaluate side-chains 228 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 143 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 394 ASN E 318 GLN E 427 GLN D 200 ASN D 442 ASN D 491 GLN B 99 GLN B 301 ASN B 316 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107057 restraints weight = 50191.717| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.70 r_work: 0.3227 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17038 Z= 0.117 Angle : 0.534 4.978 23283 Z= 0.274 Chirality : 0.044 0.254 2757 Planarity : 0.004 0.042 2873 Dihedral : 10.006 84.243 2605 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 1.03 % Allowed : 11.02 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 2003 helix: 2.90 (0.18), residues: 795 sheet: -0.34 (0.26), residues: 371 loop : 0.24 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 22 TYR 0.016 0.001 TYR D 434 PHE 0.014 0.001 PHE B 439 TRP 0.008 0.001 TRP D 62 HIS 0.006 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (17011) covalent geometry : angle 0.52116 / 0.27 (23208) SS BOND : bond 0.00742 / 0.36 ( 6) SS BOND : angle 1.34695 / 0.76 ( 12) hydrogen bonds : bond 0.04683 / 3.17 ( 881) hydrogen bonds : angle 4.57056 / 3.23 ( 2787) link_ALPHA1-3 : bond 0.00864 / 0.41 ( 2) link_ALPHA1-3 : angle 2.14397 / 1.03 ( 6) link_ALPHA1-6 : bond 0.00541 / 0.27 ( 3) link_ALPHA1-6 : angle 2.09062 / 1.25 ( 9) link_BETA1-4 : bond 0.00283 / 0.21 ( 10) link_BETA1-4 : angle 2.29957 / 1.61 ( 30) link_NAG-ASN : bond 0.00278 / 0.18 ( 6) link_NAG-ASN : angle 2.20344 / 1.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7538 (mt-10) REVERT: A 279 LEU cc_start: 0.7669 (tp) cc_final: 0.7192 (mm) REVERT: A 284 PHE cc_start: 0.8120 (t80) cc_final: 0.7802 (t80) REVERT: A 384 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6713 (mm-30) REVERT: C 104 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7546 (mppt) REVERT: C 410 LEU cc_start: 0.7979 (mm) cc_final: 0.7598 (mt) REVERT: E 10 LYS cc_start: 0.8410 (tttt) cc_final: 0.7985 (ttpt) REVERT: E 293 MET cc_start: 0.8067 (mtp) cc_final: 0.7825 (mtp) REVERT: E 321 LEU cc_start: 0.7599 (tp) cc_final: 0.7237 (tp) REVERT: E 336 ARG cc_start: 0.7730 (mmt90) cc_final: 0.7425 (mpt-90) REVERT: D 5 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: D 73 GLU cc_start: 0.7591 (tt0) cc_final: 0.6785 (tm-30) REVERT: D 167 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7281 (ttpt) REVERT: D 276 LYS cc_start: 0.8193 (mttm) cc_final: 0.7714 (mtmt) REVERT: D 436 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6892 (tm-30) REVERT: B 196 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7629 (mtt-85) REVERT: B 273 LYS cc_start: 0.7836 (tptt) cc_final: 0.7169 (mptp) REVERT: B 413 SER cc_start: 0.7713 (t) cc_final: 0.7456 (m) REVERT: B 417 GLN cc_start: 0.7060 (mt0) cc_final: 0.6796 (mt0) outliers start: 19 outliers final: 10 residues processed: 247 average time/residue: 1.1220 time to fit residues: 314.5972 Evaluate side-chains 239 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 171 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS C 164 GLN D 442 ASN D 475 GLN B 99 GLN B 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.137957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105788 restraints weight = 50410.310| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.67 r_work: 0.3180 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17038 Z= 0.183 Angle : 0.561 6.103 23283 Z= 0.288 Chirality : 0.045 0.233 2757 Planarity : 0.005 0.046 2873 Dihedral : 8.689 82.906 2604 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.30 % Rotamer: Outliers : 1.73 % Allowed : 10.96 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.19), residues: 2003 helix: 2.79 (0.17), residues: 795 sheet: -0.29 (0.25), residues: 384 loop : 0.29 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 209 TYR 0.014 0.002 TYR A 213 PHE 0.015 0.002 PHE A 105 TRP 0.012 0.001 TRP D 176 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (17011) covalent geometry : angle 0.54575 / 0.28 (23208) SS BOND : bond 0.00536 / 0.32 ( 6) SS BOND : angle 2.22598 / 1.30 ( 12) hydrogen bonds : bond 0.04930 / 3.37 ( 881) hydrogen bonds : angle 4.45089 / 3.12 ( 2787) link_ALPHA1-3 : bond 0.00628 / 0.30 ( 2) link_ALPHA1-3 : angle 1.57337 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00603 / 0.29 ( 3) link_ALPHA1-6 : angle 2.00745 / 1.13 ( 9) link_BETA1-4 : bond 0.00453 / 0.32 ( 10) link_BETA1-4 : angle 2.67103 / 1.79 ( 30) link_NAG-ASN : bond 0.00565 / 0.28 ( 6) link_NAG-ASN : angle 2.33976 / 1.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7723 (tp) cc_final: 0.7244 (mm) REVERT: A 284 PHE cc_start: 0.8185 (t80) cc_final: 0.7879 (t80) REVERT: A 324 MET cc_start: 0.4195 (mtp) cc_final: 0.3651 (pp-130) REVERT: A 384 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6794 (mm-30) REVERT: C 104 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7699 (mtpt) REVERT: C 279 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7338 (mm) REVERT: C 410 LEU cc_start: 0.8075 (mm) cc_final: 0.7697 (mt) REVERT: E 10 LYS cc_start: 0.8461 (tttt) cc_final: 0.8063 (ttpt) REVERT: E 249 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: E 275 VAL cc_start: 0.8446 (p) cc_final: 0.8220 (m) REVERT: E 293 MET cc_start: 0.8158 (mtp) cc_final: 0.7932 (mtp) REVERT: E 321 LEU cc_start: 0.7687 (tp) cc_final: 0.7329 (tp) REVERT: E 336 ARG cc_start: 0.7759 (mmt90) cc_final: 0.7490 (mpt-90) REVERT: D 5 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: D 73 GLU cc_start: 0.7551 (tt0) cc_final: 0.6919 (tm-30) REVERT: D 276 LYS cc_start: 0.8269 (mttm) cc_final: 0.7792 (mtmt) REVERT: D 431 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7857 (tt0) REVERT: D 436 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6980 (tm-30) REVERT: B 196 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7623 (mtt-85) REVERT: B 273 LYS cc_start: 0.7849 (tptt) cc_final: 0.7265 (mptp) REVERT: B 300 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7647 (ttp) REVERT: B 413 SER cc_start: 0.7722 (t) cc_final: 0.7346 (m) REVERT: B 417 GLN cc_start: 0.7102 (mt0) cc_final: 0.6777 (mt0) outliers start: 32 outliers final: 15 residues processed: 248 average time/residue: 1.1425 time to fit residues: 321.7566 Evaluate side-chains 241 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 173 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 111 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 442 ASN B 99 GLN B 226 ASN B 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104492 restraints weight = 49971.399| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.70 r_work: 0.3195 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17038 Z= 0.140 Angle : 0.517 6.368 23283 Z= 0.265 Chirality : 0.043 0.171 2757 Planarity : 0.004 0.040 2873 Dihedral : 7.561 76.993 2604 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.90 % Favored : 98.05 % Rotamer: Outliers : 1.84 % Allowed : 11.02 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.19), residues: 2003 helix: 2.85 (0.18), residues: 796 sheet: -0.27 (0.25), residues: 382 loop : 0.29 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 209 TYR 0.014 0.001 TYR A 213 PHE 0.011 0.001 PHE D 291 TRP 0.008 0.001 TRP D 176 HIS 0.007 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (17011) covalent geometry : angle 0.50464 / 0.26 (23208) SS BOND : bond 0.00374 / 0.22 ( 6) SS BOND : angle 1.68402 / 0.99 ( 12) hydrogen bonds : bond 0.04474 / 3.04 ( 881) hydrogen bonds : angle 4.30879 / 3.02 ( 2787) link_ALPHA1-3 : bond 0.00711 / 0.34 ( 2) link_ALPHA1-3 : angle 1.61062 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00634 / 0.30 ( 3) link_ALPHA1-6 : angle 1.82295 / 1.06 ( 9) link_BETA1-4 : bond 0.00369 / 0.26 ( 10) link_BETA1-4 : angle 2.30804 / 1.63 ( 30) link_NAG-ASN : bond 0.00243 / 0.12 ( 6) link_NAG-ASN : angle 1.86399 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7630 (tp) cc_final: 0.7133 (mm) REVERT: A 284 PHE cc_start: 0.8034 (t80) cc_final: 0.7742 (t80) REVERT: A 384 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6689 (mm-30) REVERT: C 104 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7558 (mtpt) REVERT: C 279 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7248 (mm) REVERT: C 410 LEU cc_start: 0.7950 (mm) cc_final: 0.7562 (mt) REVERT: E 10 LYS cc_start: 0.8437 (tttt) cc_final: 0.8008 (ttpt) REVERT: E 293 MET cc_start: 0.8067 (mtp) cc_final: 0.7842 (mtp) REVERT: E 321 LEU cc_start: 0.7661 (tp) cc_final: 0.7301 (tp) REVERT: E 336 ARG cc_start: 0.7705 (mmt90) cc_final: 0.7434 (mpt-90) REVERT: D 5 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: D 73 GLU cc_start: 0.7676 (tt0) cc_final: 0.6737 (tm-30) REVERT: D 276 LYS cc_start: 0.8211 (mttm) cc_final: 0.7720 (mtmt) REVERT: D 436 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6919 (tm-30) REVERT: B 196 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7573 (mtt-85) REVERT: B 273 LYS cc_start: 0.7808 (tptt) cc_final: 0.7200 (mptp) REVERT: B 413 SER cc_start: 0.7607 (t) cc_final: 0.7212 (m) REVERT: B 417 GLN cc_start: 0.7071 (mt0) cc_final: 0.6710 (mt0) outliers start: 34 outliers final: 14 residues processed: 246 average time/residue: 1.1215 time to fit residues: 312.5803 Evaluate side-chains 238 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 164 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN B 99 GLN B 272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103378 restraints weight = 49892.106| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.69 r_work: 0.3132 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17038 Z= 0.174 Angle : 0.540 5.141 23283 Z= 0.278 Chirality : 0.043 0.186 2757 Planarity : 0.005 0.043 2873 Dihedral : 7.352 77.014 2604 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 1.84 % Allowed : 11.23 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 2003 helix: 2.78 (0.18), residues: 796 sheet: -0.26 (0.25), residues: 377 loop : 0.26 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 209 TYR 0.015 0.002 TYR A 213 PHE 0.014 0.001 PHE A 105 TRP 0.011 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (17011) covalent geometry : angle 0.52671 / 0.27 (23208) SS BOND : bond 0.00457 / 0.27 ( 6) SS BOND : angle 1.97003 / 1.15 ( 12) hydrogen bonds : bond 0.04601 / 3.14 ( 881) hydrogen bonds : angle 4.32194 / 3.03 ( 2787) link_ALPHA1-3 : bond 0.00625 / 0.30 ( 2) link_ALPHA1-3 : angle 1.62535 / 0.82 ( 6) link_ALPHA1-6 : bond 0.00715 / 0.34 ( 3) link_ALPHA1-6 : angle 1.69664 / 1.02 ( 9) link_BETA1-4 : bond 0.00395 / 0.29 ( 10) link_BETA1-4 : angle 2.40844 / 1.68 ( 30) link_NAG-ASN : bond 0.00402 / 0.20 ( 6) link_NAG-ASN : angle 2.05674 / 1.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7928 (ttpp) REVERT: A 171 MET cc_start: 0.8012 (mtt) cc_final: 0.7810 (mtt) REVERT: A 279 LEU cc_start: 0.7716 (tp) cc_final: 0.7218 (mm) REVERT: A 284 PHE cc_start: 0.8092 (t80) cc_final: 0.7808 (t80) REVERT: A 384 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6717 (mm-30) REVERT: C 104 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7645 (mtpt) REVERT: C 279 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7310 (mm) REVERT: C 410 LEU cc_start: 0.8061 (mm) cc_final: 0.7681 (mt) REVERT: E 10 LYS cc_start: 0.8426 (tttt) cc_final: 0.8015 (ttpt) REVERT: E 293 MET cc_start: 0.8148 (mtp) cc_final: 0.7930 (mtp) REVERT: E 321 LEU cc_start: 0.7722 (tp) cc_final: 0.7406 (tp) REVERT: E 336 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7490 (mpt-90) REVERT: E 466 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7400 (t0) REVERT: D 5 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: D 46 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8252 (mppt) REVERT: D 73 GLU cc_start: 0.7685 (tt0) cc_final: 0.6833 (tm-30) REVERT: D 276 LYS cc_start: 0.8264 (mttm) cc_final: 0.7804 (mtmt) REVERT: D 431 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7838 (tt0) REVERT: D 436 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6980 (tm-30) REVERT: B 99 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7073 (tm130) REVERT: B 196 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7616 (mtt-85) REVERT: B 273 LYS cc_start: 0.7854 (tptt) cc_final: 0.7265 (mptp) REVERT: B 300 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7615 (ttp) REVERT: B 413 SER cc_start: 0.7746 (t) cc_final: 0.7464 (m) REVERT: B 417 GLN cc_start: 0.7131 (mt0) cc_final: 0.6867 (mt0) outliers start: 34 outliers final: 17 residues processed: 246 average time/residue: 1.1052 time to fit residues: 309.7503 Evaluate side-chains 245 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 475 GLN B 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103352 restraints weight = 49909.699| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.70 r_work: 0.3176 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17038 Z= 0.172 Angle : 0.539 5.082 23283 Z= 0.278 Chirality : 0.043 0.184 2757 Planarity : 0.005 0.040 2873 Dihedral : 7.320 76.007 2604 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 1.67 % Allowed : 11.61 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 2003 helix: 2.81 (0.18), residues: 796 sheet: -0.28 (0.25), residues: 377 loop : 0.24 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.016 0.002 TYR A 213 PHE 0.013 0.001 PHE A 105 TRP 0.010 0.001 TRP D 176 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (17011) covalent geometry : angle 0.52663 / 0.27 (23208) SS BOND : bond 0.00428 / 0.25 ( 6) SS BOND : angle 1.92909 / 1.13 ( 12) hydrogen bonds : bond 0.04575 / 3.12 ( 881) hydrogen bonds : angle 4.30492 / 3.02 ( 2787) link_ALPHA1-3 : bond 0.00646 / 0.31 ( 2) link_ALPHA1-3 : angle 1.60433 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00719 / 0.34 ( 3) link_ALPHA1-6 : angle 1.70282 / 1.02 ( 9) link_BETA1-4 : bond 0.00386 / 0.28 ( 10) link_BETA1-4 : angle 2.33797 / 1.65 ( 30) link_NAG-ASN : bond 0.00370 / 0.18 ( 6) link_NAG-ASN : angle 2.00608 / 1.22 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LEU cc_start: 0.7697 (tp) cc_final: 0.7193 (mm) REVERT: A 384 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6648 (mm-30) REVERT: C 104 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7557 (mppt) REVERT: C 262 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: C 279 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7269 (mm) REVERT: C 410 LEU cc_start: 0.7989 (mm) cc_final: 0.7608 (mt) REVERT: E 10 LYS cc_start: 0.8399 (tttt) cc_final: 0.7968 (ttpt) REVERT: E 249 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6731 (m-30) REVERT: E 293 MET cc_start: 0.8099 (mtp) cc_final: 0.7877 (mtp) REVERT: E 321 LEU cc_start: 0.7716 (tp) cc_final: 0.7394 (tp) REVERT: E 336 ARG cc_start: 0.7729 (mmt90) cc_final: 0.7455 (mpt-90) REVERT: E 466 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7318 (t0) REVERT: D 5 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: D 46 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8209 (mppt) REVERT: D 73 GLU cc_start: 0.7672 (tt0) cc_final: 0.6768 (tm-30) REVERT: D 167 LYS cc_start: 0.7895 (ttpp) cc_final: 0.7328 (ttpt) REVERT: D 276 LYS cc_start: 0.8239 (mttm) cc_final: 0.7771 (mtmt) REVERT: D 431 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7780 (tt0) REVERT: D 436 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6932 (tm-30) REVERT: B 196 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7572 (mtt-85) REVERT: B 273 LYS cc_start: 0.7853 (tptt) cc_final: 0.7245 (mptp) REVERT: B 300 MET cc_start: 0.8240 (ttm) cc_final: 0.7616 (ttp) REVERT: B 413 SER cc_start: 0.7671 (t) cc_final: 0.7362 (m) REVERT: B 417 GLN cc_start: 0.7084 (mt0) cc_final: 0.6814 (mt0) outliers start: 31 outliers final: 16 residues processed: 244 average time/residue: 1.1139 time to fit residues: 308.9825 Evaluate side-chains 245 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 442 ASN D 475 GLN D 491 GLN B 99 GLN B 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104740 restraints weight = 49912.750| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.70 r_work: 0.3199 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17038 Z= 0.121 Angle : 0.503 5.002 23283 Z= 0.259 Chirality : 0.042 0.179 2757 Planarity : 0.004 0.041 2873 Dihedral : 6.838 71.059 2604 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 1.40 % Allowed : 11.72 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.19), residues: 2003 helix: 3.00 (0.18), residues: 790 sheet: -0.24 (0.26), residues: 376 loop : 0.28 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.015 0.001 TYR D 434 PHE 0.012 0.001 PHE B 268 TRP 0.007 0.001 TRP D 62 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17011) covalent geometry : angle 0.49244 / 0.26 (23208) SS BOND : bond 0.00283 / 0.17 ( 6) SS BOND : angle 1.47608 / 0.86 ( 12) hydrogen bonds : bond 0.04239 / 2.87 ( 881) hydrogen bonds : angle 4.19094 / 2.94 ( 2787) link_ALPHA1-3 : bond 0.00761 / 0.36 ( 2) link_ALPHA1-3 : angle 1.52191 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00836 / 0.40 ( 3) link_ALPHA1-6 : angle 1.75432 / 1.04 ( 9) link_BETA1-4 : bond 0.00334 / 0.23 ( 10) link_BETA1-4 : angle 2.04708 / 1.47 ( 30) link_NAG-ASN : bond 0.00199 / 0.10 ( 6) link_NAG-ASN : angle 1.80329 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7835 (ttpp) REVERT: A 279 LEU cc_start: 0.7710 (tp) cc_final: 0.7200 (mm) REVERT: A 384 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6630 (mm-30) REVERT: C 104 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7551 (mtpt) REVERT: C 262 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: C 279 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7269 (mm) REVERT: C 410 LEU cc_start: 0.7975 (mm) cc_final: 0.7585 (mt) REVERT: E 10 LYS cc_start: 0.8409 (tttt) cc_final: 0.7969 (ttpt) REVERT: E 293 MET cc_start: 0.8069 (mtp) cc_final: 0.7850 (mtp) REVERT: E 321 LEU cc_start: 0.7698 (tp) cc_final: 0.7367 (tp) REVERT: E 336 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7455 (mpt-90) REVERT: E 466 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7281 (t0) REVERT: D 73 GLU cc_start: 0.7704 (tt0) cc_final: 0.6811 (tm-30) REVERT: D 276 LYS cc_start: 0.8195 (mttm) cc_final: 0.7730 (mtmt) REVERT: D 431 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7779 (tt0) REVERT: D 436 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6849 (tm-30) REVERT: B 26 GLU cc_start: 0.7943 (pm20) cc_final: 0.7734 (pm20) REVERT: B 196 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7580 (mtt-85) REVERT: B 273 LYS cc_start: 0.7939 (tptt) cc_final: 0.7311 (mptp) REVERT: B 300 MET cc_start: 0.8199 (ttm) cc_final: 0.7578 (ttp) REVERT: B 413 SER cc_start: 0.7586 (t) cc_final: 0.7295 (m) REVERT: B 417 GLN cc_start: 0.7063 (mt0) cc_final: 0.6797 (mt0) outliers start: 26 outliers final: 15 residues processed: 246 average time/residue: 1.1034 time to fit residues: 308.3450 Evaluate side-chains 241 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 181 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 164 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 475 GLN D 491 GLN B 99 GLN B 272 GLN B 417 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105375 restraints weight = 50410.702| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.67 r_work: 0.3176 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17038 Z= 0.176 Angle : 0.543 5.425 23283 Z= 0.279 Chirality : 0.043 0.183 2757 Planarity : 0.005 0.040 2873 Dihedral : 7.075 73.635 2604 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 1.30 % Allowed : 11.88 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 2003 helix: 2.85 (0.18), residues: 796 sheet: -0.26 (0.25), residues: 377 loop : 0.24 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.021 0.002 TYR A 213 PHE 0.017 0.002 PHE A 284 TRP 0.010 0.001 TRP D 176 HIS 0.008 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (17011) covalent geometry : angle 0.53110 / 0.28 (23208) SS BOND : bond 0.00449 / 0.27 ( 6) SS BOND : angle 1.94083 / 1.14 ( 12) hydrogen bonds : bond 0.04534 / 3.09 ( 881) hydrogen bonds : angle 4.27697 / 3.00 ( 2787) link_ALPHA1-3 : bond 0.00648 / 0.31 ( 2) link_ALPHA1-3 : angle 1.62985 / 0.82 ( 6) link_ALPHA1-6 : bond 0.00796 / 0.38 ( 3) link_ALPHA1-6 : angle 1.70013 / 1.02 ( 9) link_BETA1-4 : bond 0.00390 / 0.29 ( 10) link_BETA1-4 : angle 2.33402 / 1.64 ( 30) link_NAG-ASN : bond 0.00432 / 0.21 ( 6) link_NAG-ASN : angle 2.07640 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7934 (ttpp) REVERT: A 279 LEU cc_start: 0.7789 (tp) cc_final: 0.7279 (mm) REVERT: A 384 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6694 (mm-30) REVERT: C 104 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7651 (mtpt) REVERT: C 279 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7354 (mm) REVERT: C 410 LEU cc_start: 0.8078 (mm) cc_final: 0.7695 (mt) REVERT: E 10 LYS cc_start: 0.8430 (tttt) cc_final: 0.8018 (ttpt) REVERT: E 293 MET cc_start: 0.8104 (mtp) cc_final: 0.7867 (mtp) REVERT: E 321 LEU cc_start: 0.7754 (tp) cc_final: 0.7432 (tp) REVERT: E 336 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7518 (mpt-90) REVERT: E 466 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7356 (t0) REVERT: D 73 GLU cc_start: 0.7729 (tt0) cc_final: 0.6839 (tm-30) REVERT: D 167 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7382 (ttpt) REVERT: D 276 LYS cc_start: 0.8259 (mttm) cc_final: 0.7808 (mtmt) REVERT: D 431 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7829 (tt0) REVERT: D 436 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6920 (tm-30) REVERT: B 196 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7624 (mtt-85) REVERT: B 273 LYS cc_start: 0.7959 (tptt) cc_final: 0.7340 (mptp) REVERT: B 413 SER cc_start: 0.7748 (t) cc_final: 0.7452 (m) REVERT: B 417 GLN cc_start: 0.7072 (mt0) cc_final: 0.6825 (mt0) outliers start: 24 outliers final: 14 residues processed: 239 average time/residue: 1.1027 time to fit residues: 300.6370 Evaluate side-chains 237 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 164 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 442 ASN D 475 GLN D 491 GLN B 99 GLN B 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105292 restraints weight = 49936.296| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.67 r_work: 0.3177 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17038 Z= 0.174 Angle : 0.546 5.892 23283 Z= 0.282 Chirality : 0.043 0.198 2757 Planarity : 0.005 0.040 2873 Dihedral : 7.104 72.987 2604 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 1.24 % Allowed : 11.88 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.19), residues: 2003 helix: 2.86 (0.18), residues: 790 sheet: -0.30 (0.25), residues: 377 loop : 0.23 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.021 0.002 TYR A 213 PHE 0.014 0.001 PHE B 268 TRP 0.011 0.001 TRP D 176 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (17011) covalent geometry : angle 0.53450 / 0.28 (23208) SS BOND : bond 0.00423 / 0.25 ( 6) SS BOND : angle 1.90790 / 1.12 ( 12) hydrogen bonds : bond 0.04553 / 3.10 ( 881) hydrogen bonds : angle 4.29119 / 3.00 ( 2787) link_ALPHA1-3 : bond 0.00679 / 0.32 ( 2) link_ALPHA1-3 : angle 1.53756 / 0.79 ( 6) link_ALPHA1-6 : bond 0.00800 / 0.38 ( 3) link_ALPHA1-6 : angle 1.68423 / 1.01 ( 9) link_BETA1-4 : bond 0.00380 / 0.28 ( 10) link_BETA1-4 : angle 2.27096 / 1.62 ( 30) link_NAG-ASN : bond 0.00365 / 0.18 ( 6) link_NAG-ASN : angle 1.99265 / 1.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7897 (ttpp) REVERT: A 384 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6685 (mm-30) REVERT: C 104 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7642 (mtpt) REVERT: C 279 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7357 (mm) REVERT: C 410 LEU cc_start: 0.8066 (mm) cc_final: 0.7695 (mt) REVERT: E 10 LYS cc_start: 0.8423 (tttt) cc_final: 0.8012 (ttpt) REVERT: E 293 MET cc_start: 0.8142 (mtp) cc_final: 0.7890 (mtp) REVERT: E 321 LEU cc_start: 0.7743 (tp) cc_final: 0.7434 (tp) REVERT: E 336 ARG cc_start: 0.7686 (mmt90) cc_final: 0.7439 (mpt-90) REVERT: E 466 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7338 (t0) REVERT: D 73 GLU cc_start: 0.7720 (tt0) cc_final: 0.6830 (tm-30) REVERT: D 167 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7385 (ttpt) REVERT: D 276 LYS cc_start: 0.8283 (mttm) cc_final: 0.7817 (mtmt) REVERT: D 431 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7852 (tt0) REVERT: D 436 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6930 (tm-30) REVERT: B 196 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7605 (mtt-85) REVERT: B 273 LYS cc_start: 0.7947 (tptt) cc_final: 0.7333 (mptp) REVERT: B 300 MET cc_start: 0.8172 (ttm) cc_final: 0.7547 (ttp) REVERT: B 413 SER cc_start: 0.7697 (t) cc_final: 0.7367 (m) REVERT: B 417 GLN cc_start: 0.7070 (mt0) cc_final: 0.6767 (mt0) outliers start: 23 outliers final: 14 residues processed: 242 average time/residue: 1.1083 time to fit residues: 305.9750 Evaluate side-chains 240 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 20 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 HIS D 442 ASN D 475 GLN D 491 GLN B 99 GLN B 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106560 restraints weight = 50358.992| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.68 r_work: 0.3196 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17038 Z= 0.127 Angle : 0.514 6.510 23283 Z= 0.265 Chirality : 0.043 0.195 2757 Planarity : 0.004 0.040 2873 Dihedral : 6.685 68.584 2603 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 1.08 % Allowed : 12.20 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 2003 helix: 2.96 (0.18), residues: 790 sheet: -0.25 (0.26), residues: 376 loop : 0.26 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 22 TYR 0.017 0.001 TYR A 213 PHE 0.022 0.001 PHE A 284 TRP 0.007 0.001 TRP C 311 HIS 0.013 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (17011) covalent geometry : angle 0.50439 / 0.26 (23208) SS BOND : bond 0.00297 / 0.18 ( 6) SS BOND : angle 1.46462 / 0.86 ( 12) hydrogen bonds : bond 0.04259 / 2.88 ( 881) hydrogen bonds : angle 4.19029 / 2.94 ( 2787) link_ALPHA1-3 : bond 0.00769 / 0.37 ( 2) link_ALPHA1-3 : angle 1.45479 / 0.75 ( 6) link_ALPHA1-6 : bond 0.00878 / 0.42 ( 3) link_ALPHA1-6 : angle 1.74180 / 1.02 ( 9) link_BETA1-4 : bond 0.00336 / 0.23 ( 10) link_BETA1-4 : angle 2.06032 / 1.49 ( 30) link_NAG-ASN : bond 0.00231 / 0.12 ( 6) link_NAG-ASN : angle 1.84190 / 1.15 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7885 (ttpp) REVERT: A 142 CYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6765 (m) REVERT: A 279 LEU cc_start: 0.7797 (tp) cc_final: 0.7227 (mm) REVERT: A 384 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6734 (mm-30) REVERT: C 104 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7568 (mtpt) REVERT: C 279 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7357 (mm) REVERT: C 410 LEU cc_start: 0.8076 (mm) cc_final: 0.7692 (mt) REVERT: E 10 LYS cc_start: 0.8451 (tttt) cc_final: 0.8041 (ttpt) REVERT: E 293 MET cc_start: 0.8083 (mtp) cc_final: 0.7864 (mtp) REVERT: E 321 LEU cc_start: 0.7736 (tp) cc_final: 0.7433 (tp) REVERT: E 336 ARG cc_start: 0.7682 (mmt90) cc_final: 0.7456 (mpt-90) REVERT: D 73 GLU cc_start: 0.7720 (tt0) cc_final: 0.6828 (tm-30) REVERT: D 276 LYS cc_start: 0.8262 (mttm) cc_final: 0.7798 (mtmt) REVERT: D 431 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7870 (tt0) REVERT: D 436 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6910 (tm-30) REVERT: B 196 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7670 (mtt-85) REVERT: B 273 LYS cc_start: 0.7932 (tptt) cc_final: 0.7318 (mptp) REVERT: B 413 SER cc_start: 0.7574 (t) cc_final: 0.7271 (m) REVERT: B 417 GLN cc_start: 0.7072 (mt0) cc_final: 0.6778 (mt0) outliers start: 20 outliers final: 14 residues processed: 239 average time/residue: 1.0950 time to fit residues: 299.0294 Evaluate side-chains 243 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 141 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 394 ASN D 442 ASN D 475 GLN D 491 GLN B 99 GLN B 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104500 restraints weight = 50403.520| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.70 r_work: 0.3195 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 17038 Z= 0.149 Angle : 0.720 59.167 23283 Z= 0.424 Chirality : 0.043 0.183 2757 Planarity : 0.004 0.040 2873 Dihedral : 6.690 68.595 2603 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 1.08 % Allowed : 12.26 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.19), residues: 2003 helix: 2.96 (0.18), residues: 790 sheet: -0.25 (0.26), residues: 376 loop : 0.26 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.015 0.001 TYR D 434 PHE 0.013 0.001 PHE B 268 TRP 0.007 0.001 TRP C 311 HIS 0.006 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (17011) covalent geometry : angle 0.71336 / 0.42 (23208) SS BOND : bond 0.00294 / 0.17 ( 6) SS BOND : angle 1.46035 / 0.86 ( 12) hydrogen bonds : bond 0.04257 / 2.88 ( 881) hydrogen bonds : angle 4.19133 / 2.94 ( 2787) link_ALPHA1-3 : bond 0.00918 / 0.44 ( 2) link_ALPHA1-3 : angle 1.50021 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00742 / 0.36 ( 3) link_ALPHA1-6 : angle 1.70172 / 1.00 ( 9) link_BETA1-4 : bond 0.00400 / 0.25 ( 10) link_BETA1-4 : angle 2.12646 / 1.57 ( 30) link_NAG-ASN : bond 0.00234 / 0.12 ( 6) link_NAG-ASN : angle 1.84306 / 1.15 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11719.59 seconds wall clock time: 198 minutes 22.79 seconds (11902.79 seconds total)