Starting phenix.real_space_refine on Thu Mar 5 01:06:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7smt_25208/03_2026/7smt_25208.cif Found real_map, /net/cci-nas-00/data/ceres_data/7smt_25208/03_2026/7smt_25208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7smt_25208/03_2026/7smt_25208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7smt_25208/03_2026/7smt_25208.map" model { file = "/net/cci-nas-00/data/ceres_data/7smt_25208/03_2026/7smt_25208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7smt_25208/03_2026/7smt_25208.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 85 5.16 5 C 11156 2.51 5 N 2648 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17016 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 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: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'CCE': 1, 'CLR': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'DD9': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'CLR': 1, 'POV': 1, 'TC9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 CLR A 602 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 602 " occ=0.80 residue: pdb=" N POV A 603 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV A 603 " occ=0.75 residue: pdb=" N POV B 602 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 602 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" C1 CLR C 503 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 503 " occ=0.89 residue: pdb=" C1 CLR D 602 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 602 " occ=0.75 residue: pdb=" N POV D 603 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV D 603 " occ=0.75 Time building chain proxies: 4.05, per 1000 atoms: 0.24 Number of scatterers: 17016 At special positions: 0 Unit cell: (103.732, 164.688, 124.05, 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 85 16.00 P 5 15.00 O 3122 8.00 N 2648 7.00 C 11156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " 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-ASN " NAG B 601 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 797.2 milliseconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 20 sheets defined 43.7% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.840A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.125A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.514A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.909A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.883A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 371 through 426 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.860A pdb=" N THR B 68 " --> pdb=" O HIS B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.973A pdb=" N PHE B 184 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.657A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 255 through 277 removed outlier: 3.650A pdb=" N ARG B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 332 through 338 removed outlier: 4.042A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 476 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.185A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.673A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.703A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.865A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.827A pdb=" N ARG D 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.065A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.152A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.614A pdb=" N VAL D 323 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET D 324 " --> pdb=" O ILE D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 319 through 324' Processing helix chain 'D' and resid 371 through 424 Processing helix chain 'D' and resid 425 through 427 No H-bonds generated for 'chain 'D' and resid 425 through 427' Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.213A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.178A pdb=" N GLU E 73 " --> pdb=" O SER 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 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.549A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.630A pdb=" N LEU E 254 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.765A pdb=" N PHE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 472 removed outlier: 3.621A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.301A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.301A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLN A 36 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ILE A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N THR A 32 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.036A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 205 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.963A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.003A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.003A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.045A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 127 removed outlier: 6.943A pdb=" N GLU C 49 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 42 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N VAL C 174 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 35 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.253A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.253A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 81 removed outlier: 4.322A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 81 removed outlier: 4.322A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.693A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.934A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.934A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.259A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.259A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 918 hydrogen bonds defined for protein. 2664 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: 3.23 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2646 1.31 - 1.44: 4800 1.44 - 1.58: 9870 1.58 - 1.71: 11 1.71 - 1.84: 139 Bond restraints: 17466 Sorted by residual: bond pdb=" C19 TC9 D 601 " pdb=" C24 TC9 D 601 " ideal model delta sigma weight residual 1.519 1.394 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C19 TC9 D 601 " pdb=" N20 TC9 D 601 " ideal model delta sigma weight residual 1.540 1.483 0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" N POV B 602 " pdb=" C12 POV B 602 " ideal model delta sigma weight residual 1.508 1.451 0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" N POV D 603 " pdb=" C12 POV D 603 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" N POV A 603 " pdb=" C12 POV A 603 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 23388 2.38 - 4.77: 357 4.77 - 7.15: 67 7.15 - 9.53: 5 9.53 - 11.92: 10 Bond angle restraints: 23827 Sorted by residual: angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.59 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O13 POV D 603 " pdb=" P POV D 603 " pdb=" O14 POV D 603 " ideal model delta sigma weight residual 121.11 109.41 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O13 POV B 602 " pdb=" P POV B 602 " pdb=" O14 POV B 602 " ideal model delta sigma weight residual 121.11 109.48 11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O13 POV C 501 " pdb=" P POV C 501 " pdb=" O14 POV C 501 " ideal model delta sigma weight residual 121.11 109.52 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.25 -11.58 3.00e+00 1.11e-01 1.49e+01 ... (remaining 23822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 10453 30.32 - 60.65: 296 60.65 - 90.97: 59 90.97 - 121.29: 21 121.29 - 151.62: 5 Dihedral angle restraints: 10834 sinusoidal: 4835 harmonic: 5999 Sorted by residual: dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 10831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2498 0.075 - 0.151: 290 0.151 - 0.226: 11 0.226 - 0.302: 7 0.302 - 0.377: 1 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 141 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2804 not shown) Planarity restraints: 2889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 223 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C ILE E 223 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE E 223 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE E 224 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 TC9 D 601 " -0.014 2.00e-02 2.50e+03 1.03e-02 2.91e+00 pdb=" C22 TC9 D 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 D 601 " -0.012 2.00e-02 2.50e+03 pdb=" C24 TC9 D 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 D 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 D 601 " -0.000 2.00e-02 2.50e+03 pdb=" C27 TC9 D 601 " -0.002 2.00e-02 2.50e+03 pdb=" C28 TC9 D 601 " -0.015 2.00e-02 2.50e+03 pdb=" O29 TC9 D 601 " 0.014 2.00e-02 2.50e+03 pdb=" O40 TC9 D 601 " 0.001 2.00e-02 2.50e+03 pdb=" O42 TC9 D 601 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 221 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ILE C 221 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 221 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 222 " 0.010 2.00e-02 2.50e+03 ... (remaining 2886 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1307 2.74 - 3.28: 16520 3.28 - 3.82: 28725 3.82 - 4.36: 35156 4.36 - 4.90: 60417 Nonbonded interactions: 142125 Sorted by model distance: nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP D 152 " pdb=" OG1 THR D 154 " model vdw 2.208 3.040 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG SER B 129 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 494 " pdb=" OD1 ASP B 496 " model vdw 2.222 3.040 nonbonded pdb=" OE2 GLU D 45 " pdb=" NH2 ARG D 209 " model vdw 2.246 3.120 ... (remaining 142120 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 426 or resid 602 or (resid 603 and (name N or na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or n \ ame O31 or name O32 or name P )))) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426 or resid 602 or (re \ sid 603 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.660 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 17495 Z= 0.263 Angle : 0.751 11.919 23907 Z= 0.334 Chirality : 0.049 0.377 2807 Planarity : 0.004 0.039 2882 Dihedral : 16.078 151.617 6907 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.12 (0.19), residues: 2002 helix: 2.44 (0.18), residues: 759 sheet: 0.24 (0.25), residues: 405 loop : -0.58 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 217 TYR 0.018 0.002 TYR D 93 PHE 0.018 0.002 PHE E 422 TRP 0.014 0.001 TRP C 317 HIS 0.006 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00577 (17466) covalent geometry : angle 0.73959 (23827) SS BOND : bond 0.00750 ( 7) SS BOND : angle 1.94443 ( 14) hydrogen bonds : bond 0.12557 ( 837) hydrogen bonds : angle 5.65859 ( 2664) link_ALPHA1-6 : bond 0.00419 ( 6) link_ALPHA1-6 : angle 1.65552 ( 18) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 2.25847 ( 27) link_NAG-ASN : bond 0.00399 ( 7) link_NAG-ASN : angle 3.06602 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.621 Fit side-chains REVERT: A 17 LYS cc_start: 0.9029 (pttt) cc_final: 0.8808 (pttp) REVERT: A 127 TYR cc_start: 0.8477 (t80) cc_final: 0.8120 (t80) REVERT: A 243 MET cc_start: 0.9034 (mmm) cc_final: 0.8743 (mmm) REVERT: A 278 MET cc_start: 0.8079 (mmm) cc_final: 0.7655 (mmm) REVERT: A 373 LYS cc_start: 0.8283 (pttp) cc_final: 0.7805 (mptt) REVERT: B 46 LYS cc_start: 0.8317 (mmtp) cc_final: 0.7914 (mtmt) REVERT: C 288 MET cc_start: 0.8572 (ttm) cc_final: 0.8313 (mtp) REVERT: D 97 ASP cc_start: 0.7567 (t0) cc_final: 0.7275 (t0) REVERT: D 178 MET cc_start: 0.8941 (mmp) cc_final: 0.8571 (tpp) REVERT: E 425 LYS cc_start: 0.8215 (ttmm) cc_final: 0.8014 (ttpp) outliers start: 0 outliers final: 2 residues processed: 209 average time/residue: 0.7128 time to fit residues: 164.0367 Evaluate side-chains 133 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain E residue 413 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN B 305 ASN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.066679 restraints weight = 29079.630| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.18 r_work: 0.2732 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17495 Z= 0.162 Angle : 0.569 8.339 23907 Z= 0.286 Chirality : 0.044 0.294 2807 Planarity : 0.004 0.035 2882 Dihedral : 13.189 135.679 2989 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.50 % Allowed : 6.21 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.35 (0.19), residues: 2002 helix: 2.66 (0.18), residues: 771 sheet: 0.28 (0.26), residues: 408 loop : -0.48 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 217 TYR 0.014 0.001 TYR D 93 PHE 0.015 0.001 PHE D 284 TRP 0.009 0.001 TRP D 60 HIS 0.003 0.001 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00371 (17466) covalent geometry : angle 0.55104 (23827) SS BOND : bond 0.01002 ( 7) SS BOND : angle 3.33817 ( 14) hydrogen bonds : bond 0.05146 ( 837) hydrogen bonds : angle 4.32111 ( 2664) link_ALPHA1-6 : bond 0.00657 ( 6) link_ALPHA1-6 : angle 1.87384 ( 18) link_BETA1-4 : bond 0.00430 ( 9) link_BETA1-4 : angle 2.20951 ( 27) link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 2.59529 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 42 SER cc_start: 0.8969 (t) cc_final: 0.8765 (p) REVERT: A 127 TYR cc_start: 0.8729 (t80) cc_final: 0.8281 (t80) REVERT: A 278 MET cc_start: 0.8648 (mmm) cc_final: 0.8441 (mmm) REVERT: B 46 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8041 (mtmt) REVERT: B 186 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: B 420 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7482 (ttpp) REVERT: B 475 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8465 (ttt) REVERT: C 311 THR cc_start: 0.8301 (m) cc_final: 0.8055 (p) REVERT: D 97 ASP cc_start: 0.8314 (t0) cc_final: 0.7994 (t0) REVERT: D 324 MET cc_start: 0.7591 (mtm) cc_final: 0.7301 (ptp) REVERT: D 329 MET cc_start: 0.7657 (mtt) cc_final: 0.7371 (mtt) REVERT: E 414 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5585 (tptt) REVERT: E 425 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7946 (ttpp) outliers start: 28 outliers final: 9 residues processed: 162 average time/residue: 0.6218 time to fit residues: 112.1948 Evaluate side-chains 139 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 170 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 28 ASN B 276 GLN D 408 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.086871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.065927 restraints weight = 29109.194| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.17 r_work: 0.2709 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17495 Z= 0.181 Angle : 0.565 7.670 23907 Z= 0.282 Chirality : 0.045 0.286 2807 Planarity : 0.004 0.035 2882 Dihedral : 11.648 123.399 2985 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.98 % Allowed : 7.76 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.38 (0.19), residues: 2002 helix: 2.72 (0.18), residues: 772 sheet: 0.30 (0.26), residues: 407 loop : -0.53 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 217 TYR 0.015 0.001 TYR D 93 PHE 0.015 0.001 PHE D 284 TRP 0.009 0.001 TRP D 60 HIS 0.005 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00426 (17466) covalent geometry : angle 0.54869 (23827) SS BOND : bond 0.00924 ( 7) SS BOND : angle 2.69646 ( 14) hydrogen bonds : bond 0.05033 ( 837) hydrogen bonds : angle 4.14863 ( 2664) link_ALPHA1-6 : bond 0.00540 ( 6) link_ALPHA1-6 : angle 1.79610 ( 18) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 2.29223 ( 27) link_NAG-ASN : bond 0.00284 ( 7) link_NAG-ASN : angle 2.67330 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8707 (t80) cc_final: 0.8276 (t80) REVERT: A 386 MET cc_start: 0.8718 (mmm) cc_final: 0.8500 (mtp) REVERT: A 387 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8250 (tppt) REVERT: B 46 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8048 (mtmt) REVERT: B 186 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: B 420 LYS cc_start: 0.7790 (ttmt) cc_final: 0.7487 (ttpp) REVERT: B 475 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8481 (ttt) REVERT: D 97 ASP cc_start: 0.8374 (t0) cc_final: 0.8078 (t0) REVERT: D 324 MET cc_start: 0.7705 (mtm) cc_final: 0.7400 (ptp) REVERT: D 377 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: E 414 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5625 (tptt) outliers start: 37 outliers final: 18 residues processed: 156 average time/residue: 0.6344 time to fit residues: 110.3950 Evaluate side-chains 148 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 2 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.066378 restraints weight = 28950.572| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.17 r_work: 0.2727 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17495 Z= 0.162 Angle : 0.549 8.063 23907 Z= 0.273 Chirality : 0.044 0.284 2807 Planarity : 0.003 0.034 2882 Dihedral : 10.561 118.787 2985 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.03 % Allowed : 8.40 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.46 (0.19), residues: 2002 helix: 2.81 (0.18), residues: 772 sheet: 0.30 (0.25), residues: 407 loop : -0.48 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 217 TYR 0.012 0.001 TYR E 117 PHE 0.014 0.001 PHE D 284 TRP 0.009 0.001 TRP A 60 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00376 (17466) covalent geometry : angle 0.53083 (23827) SS BOND : bond 0.01285 ( 7) SS BOND : angle 3.17970 ( 14) hydrogen bonds : bond 0.04783 ( 837) hydrogen bonds : angle 4.03024 ( 2664) link_ALPHA1-6 : bond 0.00640 ( 6) link_ALPHA1-6 : angle 1.81078 ( 18) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 2.23506 ( 27) link_NAG-ASN : bond 0.00199 ( 7) link_NAG-ASN : angle 2.61451 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.578 Fit side-chains REVERT: A 127 TYR cc_start: 0.8709 (t80) cc_final: 0.8289 (t80) REVERT: A 386 MET cc_start: 0.8762 (mmm) cc_final: 0.8542 (mtp) REVERT: A 387 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8208 (mttp) REVERT: A 397 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: B 46 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8029 (mtmt) REVERT: B 186 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: B 420 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7495 (ttpp) REVERT: B 475 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8482 (ttt) REVERT: D 97 ASP cc_start: 0.8356 (t0) cc_final: 0.8054 (t0) REVERT: D 324 MET cc_start: 0.7848 (mtm) cc_final: 0.7519 (ptp) REVERT: D 377 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: E 177 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: E 469 THR cc_start: 0.8900 (t) cc_final: 0.8531 (p) outliers start: 38 outliers final: 15 residues processed: 156 average time/residue: 0.6175 time to fit residues: 107.4914 Evaluate side-chains 146 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 184 optimal weight: 0.2980 chunk 157 optimal weight: 0.8980 chunk 95 optimal weight: 0.0570 chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN D 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.068460 restraints weight = 28605.240| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.17 r_work: 0.2758 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 17495 Z= 0.110 Angle : 0.513 9.411 23907 Z= 0.257 Chirality : 0.043 0.277 2807 Planarity : 0.003 0.034 2882 Dihedral : 9.599 119.257 2985 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.77 % Allowed : 9.90 % Favored : 88.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.63 % 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: 1.62 (0.19), residues: 2002 helix: 2.97 (0.18), residues: 771 sheet: 0.40 (0.26), residues: 391 loop : -0.41 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 336 TYR 0.015 0.001 TYR E 117 PHE 0.014 0.001 PHE D 284 TRP 0.010 0.001 TRP A 60 HIS 0.003 0.000 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00242 (17466) covalent geometry : angle 0.49475 (23827) SS BOND : bond 0.00949 ( 7) SS BOND : angle 3.63519 ( 14) hydrogen bonds : bond 0.04256 ( 837) hydrogen bonds : angle 3.81471 ( 2664) link_ALPHA1-6 : bond 0.00725 ( 6) link_ALPHA1-6 : angle 1.73229 ( 18) link_BETA1-4 : bond 0.00459 ( 9) link_BETA1-4 : angle 1.93842 ( 27) link_NAG-ASN : bond 0.00157 ( 7) link_NAG-ASN : angle 2.42557 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.646 Fit side-chains REVERT: A 127 TYR cc_start: 0.8687 (t80) cc_final: 0.8289 (t80) REVERT: A 208 GLN cc_start: 0.8910 (tp40) cc_final: 0.8692 (tp40) REVERT: A 387 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8182 (mttp) REVERT: A 397 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: B 46 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8022 (mtmt) REVERT: B 186 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: B 420 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7393 (ttpp) REVERT: B 475 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8452 (ttt) REVERT: B 499 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7880 (ptp-170) REVERT: C 422 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: D 97 ASP cc_start: 0.8297 (t0) cc_final: 0.7991 (t0) REVERT: D 163 ASP cc_start: 0.8879 (m-30) cc_final: 0.8570 (t0) REVERT: D 200 ASP cc_start: 0.8328 (t70) cc_final: 0.8080 (p0) REVERT: D 324 MET cc_start: 0.7896 (mtm) cc_final: 0.7433 (ptp) REVERT: D 377 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: E 166 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6876 (pp20) REVERT: E 292 PHE cc_start: 0.8554 (t80) cc_final: 0.7960 (m-80) REVERT: E 414 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.5606 (tptt) REVERT: E 469 THR cc_start: 0.8866 (t) cc_final: 0.8501 (p) outliers start: 33 outliers final: 9 residues processed: 165 average time/residue: 0.6121 time to fit residues: 113.0289 Evaluate side-chains 146 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 50 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 162 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN D 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.068428 restraints weight = 28709.260| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.17 r_work: 0.2770 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 17495 Z= 0.115 Angle : 0.513 10.476 23907 Z= 0.256 Chirality : 0.043 0.267 2807 Planarity : 0.003 0.034 2882 Dihedral : 9.095 120.289 2985 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.98 % Allowed : 10.12 % Favored : 87.90 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.63 % 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: 1.70 (0.19), residues: 2002 helix: 3.02 (0.18), residues: 771 sheet: 0.41 (0.26), residues: 394 loop : -0.33 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 336 TYR 0.013 0.001 TYR E 117 PHE 0.013 0.001 PHE D 284 TRP 0.009 0.001 TRP A 311 HIS 0.011 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00260 (17466) covalent geometry : angle 0.49582 (23827) SS BOND : bond 0.00990 ( 7) SS BOND : angle 3.50075 ( 14) hydrogen bonds : bond 0.04159 ( 837) hydrogen bonds : angle 3.75355 ( 2664) link_ALPHA1-6 : bond 0.00716 ( 6) link_ALPHA1-6 : angle 1.70655 ( 18) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.99859 ( 27) link_NAG-ASN : bond 0.00115 ( 7) link_NAG-ASN : angle 2.32977 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.637 Fit side-chains REVERT: A 127 TYR cc_start: 0.8661 (t80) cc_final: 0.8266 (t80) REVERT: A 208 GLN cc_start: 0.8918 (tp40) cc_final: 0.8677 (tp40) REVERT: A 222 CYS cc_start: 0.8373 (t) cc_final: 0.8099 (m) REVERT: A 387 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8256 (mttp) REVERT: A 397 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 46 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8039 (mtmt) REVERT: B 186 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: B 420 LYS cc_start: 0.7635 (ttmt) cc_final: 0.7318 (ttpp) REVERT: B 475 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8455 (ttt) REVERT: B 499 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7885 (ptp-170) REVERT: C 422 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: D 97 ASP cc_start: 0.8300 (t0) cc_final: 0.7996 (t0) REVERT: D 163 ASP cc_start: 0.8874 (m-30) cc_final: 0.8567 (t0) REVERT: D 200 ASP cc_start: 0.8330 (t70) cc_final: 0.8106 (p0) REVERT: D 324 MET cc_start: 0.7852 (mtm) cc_final: 0.7451 (ptp) REVERT: D 373 LYS cc_start: 0.6598 (mptt) cc_final: 0.5526 (mptt) REVERT: D 377 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: E 166 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: E 292 PHE cc_start: 0.8551 (t80) cc_final: 0.7948 (m-80) REVERT: E 469 THR cc_start: 0.8838 (t) cc_final: 0.8448 (p) outliers start: 37 outliers final: 17 residues processed: 164 average time/residue: 0.6301 time to fit residues: 115.1856 Evaluate side-chains 154 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN B 432 GLN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.066936 restraints weight = 28801.417| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.19 r_work: 0.2725 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 17495 Z= 0.153 Angle : 0.543 11.811 23907 Z= 0.271 Chirality : 0.044 0.262 2807 Planarity : 0.003 0.034 2882 Dihedral : 8.924 120.629 2985 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 10.17 % Favored : 87.90 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.63 % 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: 1.61 (0.19), residues: 2002 helix: 2.95 (0.18), residues: 771 sheet: 0.32 (0.25), residues: 403 loop : -0.37 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 336 TYR 0.013 0.001 TYR E 117 PHE 0.014 0.001 PHE D 284 TRP 0.009 0.001 TRP A 311 HIS 0.011 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00361 (17466) covalent geometry : angle 0.52235 (23827) SS BOND : bond 0.01115 ( 7) SS BOND : angle 4.14226 ( 14) hydrogen bonds : bond 0.04414 ( 837) hydrogen bonds : angle 3.84531 ( 2664) link_ALPHA1-6 : bond 0.00651 ( 6) link_ALPHA1-6 : angle 1.71675 ( 18) link_BETA1-4 : bond 0.00375 ( 9) link_BETA1-4 : angle 2.15295 ( 27) link_NAG-ASN : bond 0.00182 ( 7) link_NAG-ASN : angle 2.39836 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8679 (t80) cc_final: 0.8275 (t80) REVERT: A 208 GLN cc_start: 0.8908 (tp40) cc_final: 0.8682 (tp40) REVERT: A 222 CYS cc_start: 0.8437 (t) cc_final: 0.8175 (m) REVERT: A 387 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8176 (mtmm) REVERT: A 397 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: B 46 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8011 (mtmt) REVERT: B 186 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: B 475 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (ttt) REVERT: B 499 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8155 (ptp-170) REVERT: C 422 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: D 97 ASP cc_start: 0.8325 (t0) cc_final: 0.8007 (t0) REVERT: D 163 ASP cc_start: 0.8856 (m-30) cc_final: 0.8561 (t0) REVERT: D 324 MET cc_start: 0.7865 (mtm) cc_final: 0.7418 (ptp) REVERT: E 166 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6780 (pp20) REVERT: E 177 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: E 292 PHE cc_start: 0.8557 (t80) cc_final: 0.7948 (m-80) REVERT: E 414 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.5567 (tptt) REVERT: E 469 THR cc_start: 0.8853 (t) cc_final: 0.8414 (p) outliers start: 36 outliers final: 18 residues processed: 156 average time/residue: 0.6456 time to fit residues: 112.6142 Evaluate side-chains 152 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN D 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.088862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.067796 restraints weight = 28659.149| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.18 r_work: 0.2757 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.178 17495 Z= 0.136 Angle : 0.570 18.993 23907 Z= 0.287 Chirality : 0.043 0.271 2807 Planarity : 0.003 0.034 2882 Dihedral : 8.559 120.763 2985 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.93 % Allowed : 10.28 % Favored : 87.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.66 (0.19), residues: 2002 helix: 3.00 (0.18), residues: 771 sheet: 0.33 (0.25), residues: 406 loop : -0.33 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 336 TYR 0.014 0.001 TYR E 117 PHE 0.013 0.001 PHE D 284 TRP 0.010 0.001 TRP A 311 HIS 0.010 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00335 (17466) covalent geometry : angle 0.53888 (23827) SS BOND : bond 0.01696 ( 7) SS BOND : angle 6.46067 ( 14) hydrogen bonds : bond 0.04162 ( 837) hydrogen bonds : angle 3.75154 ( 2664) link_ALPHA1-6 : bond 0.00720 ( 6) link_ALPHA1-6 : angle 1.62680 ( 18) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 1.97705 ( 27) link_NAG-ASN : bond 0.00106 ( 7) link_NAG-ASN : angle 2.32458 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.665 Fit side-chains REVERT: A 127 TYR cc_start: 0.8657 (t80) cc_final: 0.8263 (t80) REVERT: A 208 GLN cc_start: 0.8947 (tp40) cc_final: 0.8686 (tp-100) REVERT: A 222 CYS cc_start: 0.8211 (t) cc_final: 0.8003 (m) REVERT: A 387 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8151 (mtmm) REVERT: A 397 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: B 46 LYS cc_start: 0.8696 (mmtp) cc_final: 0.7993 (mtmt) REVERT: B 186 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: B 475 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8496 (ttt) REVERT: B 499 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7807 (ptp-170) REVERT: C 422 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: D 97 ASP cc_start: 0.8285 (t0) cc_final: 0.7962 (t0) REVERT: D 163 ASP cc_start: 0.8833 (m-30) cc_final: 0.8542 (t0) REVERT: D 200 ASP cc_start: 0.8373 (t70) cc_final: 0.8138 (p0) REVERT: E 166 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6772 (pp20) REVERT: E 177 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: E 292 PHE cc_start: 0.8536 (t80) cc_final: 0.7933 (m-80) REVERT: E 414 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.5537 (tptt) REVERT: E 469 THR cc_start: 0.8854 (t) cc_final: 0.8425 (p) outliers start: 36 outliers final: 17 residues processed: 153 average time/residue: 0.5975 time to fit residues: 102.4195 Evaluate side-chains 151 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 50 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN B 313 HIS D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.068677 restraints weight = 28607.706| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.18 r_work: 0.2776 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 17495 Z= 0.132 Angle : 0.572 19.261 23907 Z= 0.287 Chirality : 0.043 0.293 2807 Planarity : 0.003 0.034 2882 Dihedral : 8.201 121.054 2985 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.87 % Allowed : 10.60 % Favored : 87.53 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 2002 helix: 3.05 (0.18), residues: 772 sheet: 0.44 (0.26), residues: 395 loop : -0.30 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 336 TYR 0.013 0.001 TYR E 117 PHE 0.013 0.001 PHE D 284 TRP 0.011 0.001 TRP A 311 HIS 0.009 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00334 (17466) covalent geometry : angle 0.53546 (23827) SS BOND : bond 0.01870 ( 7) SS BOND : angle 7.28490 ( 14) hydrogen bonds : bond 0.03963 ( 837) hydrogen bonds : angle 3.66654 ( 2664) link_ALPHA1-6 : bond 0.00728 ( 6) link_ALPHA1-6 : angle 1.59930 ( 18) link_BETA1-4 : bond 0.00447 ( 9) link_BETA1-4 : angle 1.88910 ( 27) link_NAG-ASN : bond 0.00114 ( 7) link_NAG-ASN : angle 2.19997 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.659 Fit side-chains REVERT: A 127 TYR cc_start: 0.8643 (t80) cc_final: 0.8273 (t80) REVERT: A 208 GLN cc_start: 0.8944 (tp40) cc_final: 0.8703 (tp-100) REVERT: A 387 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8116 (mtmm) REVERT: A 397 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: B 46 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8036 (mtmt) REVERT: B 186 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: B 475 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8397 (ttt) REVERT: B 499 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7904 (ptp-170) REVERT: D 97 ASP cc_start: 0.8257 (t0) cc_final: 0.7941 (t0) REVERT: D 163 ASP cc_start: 0.8808 (m-30) cc_final: 0.8534 (t0) REVERT: D 200 ASP cc_start: 0.8364 (t70) cc_final: 0.8157 (p0) REVERT: E 166 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6803 (pp20) REVERT: E 177 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: E 292 PHE cc_start: 0.8530 (t80) cc_final: 0.7941 (m-80) REVERT: E 414 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5522 (tptt) REVERT: E 469 THR cc_start: 0.8835 (t) cc_final: 0.8400 (p) outliers start: 35 outliers final: 16 residues processed: 155 average time/residue: 0.6474 time to fit residues: 111.7964 Evaluate side-chains 151 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 58 optimal weight: 0.0170 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN B 276 GLN B 339 HIS D 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.089222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.068070 restraints weight = 28564.453| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.20 r_work: 0.2757 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 17495 Z= 0.150 Angle : 0.596 19.134 23907 Z= 0.298 Chirality : 0.043 0.274 2807 Planarity : 0.003 0.048 2882 Dihedral : 8.108 121.080 2985 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.55 % Allowed : 11.13 % Favored : 87.31 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 2002 helix: 3.03 (0.18), residues: 772 sheet: 0.38 (0.25), residues: 404 loop : -0.31 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 336 TYR 0.013 0.001 TYR E 117 PHE 0.014 0.001 PHE B 471 TRP 0.011 0.001 TRP A 311 HIS 0.009 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00383 (17466) covalent geometry : angle 0.55991 (23827) SS BOND : bond 0.01767 ( 7) SS BOND : angle 7.33807 ( 14) hydrogen bonds : bond 0.04104 ( 837) hydrogen bonds : angle 3.72937 ( 2664) link_ALPHA1-6 : bond 0.00693 ( 6) link_ALPHA1-6 : angle 1.60228 ( 18) link_BETA1-4 : bond 0.00391 ( 9) link_BETA1-4 : angle 1.97432 ( 27) link_NAG-ASN : bond 0.00151 ( 7) link_NAG-ASN : angle 2.23502 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.635 Fit side-chains REVERT: A 127 TYR cc_start: 0.8651 (t80) cc_final: 0.8276 (t80) REVERT: A 208 GLN cc_start: 0.8969 (tp40) cc_final: 0.8730 (tp-100) REVERT: A 387 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8152 (mtmm) REVERT: A 397 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: B 46 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8031 (mtmt) REVERT: B 186 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: B 475 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (ttt) REVERT: B 499 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7789 (ptp-170) REVERT: D 97 ASP cc_start: 0.8293 (t0) cc_final: 0.7979 (t0) REVERT: D 163 ASP cc_start: 0.8828 (m-30) cc_final: 0.8544 (t0) REVERT: D 200 ASP cc_start: 0.8386 (t70) cc_final: 0.8143 (p0) REVERT: E 166 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6807 (pp20) REVERT: E 177 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: E 292 PHE cc_start: 0.8546 (t80) cc_final: 0.7948 (m-80) REVERT: E 469 THR cc_start: 0.8822 (t) cc_final: 0.8380 (p) outliers start: 29 outliers final: 17 residues processed: 150 average time/residue: 0.6476 time to fit residues: 108.3037 Evaluate side-chains 150 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 3 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN D 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.067483 restraints weight = 28623.938| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.17 r_work: 0.2751 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 17495 Z= 0.155 Angle : 0.597 19.398 23907 Z= 0.298 Chirality : 0.044 0.274 2807 Planarity : 0.003 0.040 2882 Dihedral : 8.060 121.030 2985 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.66 % Allowed : 11.35 % Favored : 86.99 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.69 (0.19), residues: 2002 helix: 3.00 (0.18), residues: 772 sheet: 0.38 (0.25), residues: 404 loop : -0.32 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 336 TYR 0.013 0.001 TYR E 117 PHE 0.013 0.001 PHE D 284 TRP 0.008 0.001 TRP A 60 HIS 0.009 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00392 (17466) covalent geometry : angle 0.56201 (23827) SS BOND : bond 0.01705 ( 7) SS BOND : angle 7.18996 ( 14) hydrogen bonds : bond 0.04169 ( 837) hydrogen bonds : angle 3.75643 ( 2664) link_ALPHA1-6 : bond 0.00691 ( 6) link_ALPHA1-6 : angle 1.59014 ( 18) link_BETA1-4 : bond 0.00383 ( 9) link_BETA1-4 : angle 2.00188 ( 27) link_NAG-ASN : bond 0.00158 ( 7) link_NAG-ASN : angle 2.26927 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5983.00 seconds wall clock time: 102 minutes 38.12 seconds (6158.12 seconds total)