Starting phenix.real_space_refine on Thu Sep 18 07:11:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ffm_50366/09_2025/9ffm_50366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ffm_50366/09_2025/9ffm_50366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ffm_50366/09_2025/9ffm_50366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ffm_50366/09_2025/9ffm_50366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ffm_50366/09_2025/9ffm_50366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ffm_50366/09_2025/9ffm_50366.map" } resolution = 3.0 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= 0.007 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9714 2.51 5 N 2425 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14962 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 2722 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Conformer: "B" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} bond proxies already assigned to first conformer: 2774 Chain: "E" Number of atoms: 2739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Conformer: "B" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} bond proxies already assigned to first conformer: 2793 Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "A" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 2747 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Conformer: "B" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} bond proxies already assigned to first conformer: 2783 Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.36 Number of scatterers: 14962 At special positions: 0 Unit cell: (94.2339, 122.752, 128.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2739 8.00 N 2425 7.00 C 9714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 484 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG G 1 " - " ASN E 80 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN C 80 " " NAG a 1 " - " ASN D 111 " " NAG b 1 " - " ASN E 149 " " NAG c 1 " - " ASN B 149 " " NAG d 1 " - " ASN A 111 " " NAG e 1 " - " ASN C 149 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 941.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 21 sheets defined 40.8% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.717A pdb=" N THR D 16 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.839A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.605A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.802A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.576A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 removed outlier: 3.541A pdb=" N PHE D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 417 removed outlier: 3.559A pdb=" N ARG D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.524A pdb=" N TYR D 415 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.651A pdb=" N ALA E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.788A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 236 removed outlier: 3.557A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.517A pdb=" N ILE E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 272 removed outlier: 3.805A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR E 271 " --> pdb=" O HIS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 306 removed outlier: 4.018A pdb=" N TYR E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 447 removed outlier: 3.990A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 431 " --> pdb=" O SER E 427 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.755A pdb=" N ALA B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.707A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 removed outlier: 3.571A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 246 through 267 removed outlier: 3.501A pdb=" N VAL B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 306 removed outlier: 3.773A pdb=" N MET B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 447 removed outlier: 3.801A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.685A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.525A pdb=" N SER A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.572A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 251 through 277 removed outlier: 3.507A pdb=" N ASN A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.529A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 417 removed outlier: 3.652A pdb=" N ARG A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 3.660A pdb=" N ASN A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.530A pdb=" N ALA C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.626A pdb=" N ALA C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.440A pdb=" N ARG C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.951A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.858A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.556A pdb=" N VAL C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 306 removed outlier: 3.549A pdb=" N PHE C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 447 removed outlier: 4.019A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 431 " --> pdb=" O SER C 427 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'F' and resid 450 through 453 removed outlier: 3.545A pdb=" N LYS F 453 " --> pdb=" O ASP F 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 450 through 453' Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing sheet with id=AA1, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.134A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.142A pdb=" N ASP D 63 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE D 50 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N PHE D 65 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR D 48 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ARG D 67 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE D 46 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER D 69 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP D 44 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N LYS D 71 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N LYS D 42 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.355A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.355A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.746A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.660A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.021A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.021A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.825A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR B 60 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 47 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR B 62 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA B 45 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLN B 64 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP B 43 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N TYR B 66 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASN B 41 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ARG B 68 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N GLY B 39 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 167 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.749A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR B 60 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 47 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR B 62 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA B 45 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLN B 64 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP B 43 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N TYR B 66 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASN B 41 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ARG B 68 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N GLY B 39 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.022A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.022A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.984A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 46 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 108 through 109 removed outlier: 7.112A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 46 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.566A pdb=" N HIS A 151 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.846A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.857A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.051A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AC2, first strand: chain 'F' and resid 446 through 448 removed outlier: 5.483A pdb=" N PHE F 435 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG F 426 " --> pdb=" O PHE F 435 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY F 437 " --> pdb=" O TRP F 424 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 421 " --> pdb=" O LYS F 487 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS F 484 " --> pdb=" O TRP F 503 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP F 503 " --> pdb=" O CYS F 484 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA F 486 " --> pdb=" O ASP F 501 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 446 through 448 removed outlier: 5.483A pdb=" N PHE F 435 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG F 426 " --> pdb=" O PHE F 435 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY F 437 " --> pdb=" O TRP F 424 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 421 " --> pdb=" O LYS F 487 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA F 480 " --> pdb=" O VAL F 509 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL F 509 " --> pdb=" O ALA F 480 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4558 1.34 - 1.46: 3734 1.46 - 1.58: 6911 1.58 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 15349 Sorted by residual: bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 MAN e 5 " pdb=" O5 MAN e 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 MAN d 5 " pdb=" O5 MAN d 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C1 MAN c 5 " pdb=" O5 MAN c 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 MAN b 5 " pdb=" O5 MAN b 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.48e+00 ... (remaining 15344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 20219 1.13 - 2.25: 430 2.25 - 3.38: 174 3.38 - 4.50: 30 4.50 - 5.63: 17 Bond angle restraints: 20870 Sorted by residual: angle pdb=" N ARG A 173 " pdb=" CA ARG A 173 " pdb=" C ARG A 173 " ideal model delta sigma weight residual 110.80 106.80 4.00 2.13e+00 2.20e-01 3.53e+00 angle pdb=" C1 BMA e 3 " pdb=" O5 BMA e 3 " pdb=" C5 BMA e 3 " ideal model delta sigma weight residual 118.82 113.19 5.63 3.00e+00 1.11e-01 3.52e+00 angle pdb=" C1 BMA c 3 " pdb=" O5 BMA c 3 " pdb=" C5 BMA c 3 " ideal model delta sigma weight residual 118.82 113.22 5.60 3.00e+00 1.11e-01 3.49e+00 angle pdb=" C1 BMA a 3 " pdb=" O5 BMA a 3 " pdb=" C5 BMA a 3 " ideal model delta sigma weight residual 118.82 113.37 5.45 3.00e+00 1.11e-01 3.30e+00 angle pdb=" C1 BMA b 3 " pdb=" O5 BMA b 3 " pdb=" C5 BMA b 3 " ideal model delta sigma weight residual 118.82 113.43 5.39 3.00e+00 1.11e-01 3.23e+00 ... (remaining 20865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 9140 21.15 - 42.31: 216 42.31 - 63.46: 21 63.46 - 84.61: 32 84.61 - 105.77: 20 Dihedral angle restraints: 9429 sinusoidal: 4140 harmonic: 5289 Sorted by residual: dihedral pdb=" CA PRO C 276 " pdb=" C PRO C 276 " pdb=" N TYR C 277 " pdb=" CA TYR C 277 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" O4 BMA e 3 " pdb=" C4 BMA e 3 " pdb=" C5 BMA e 3 " pdb=" O5 BMA e 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.06 105.77 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C5 BMA d 3 " pdb=" O5 BMA d 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.94 105.65 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1978 0.048 - 0.096: 317 0.096 - 0.145: 132 0.145 - 0.193: 3 0.193 - 0.241: 5 Chirality restraints: 2435 Sorted by residual: chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2432 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 275 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B 276 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO E 276 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 275 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO C 276 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 276 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 276 " -0.020 5.00e-02 4.00e+02 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3669 2.80 - 3.32: 13047 3.32 - 3.85: 23921 3.85 - 4.37: 28932 4.37 - 4.90: 50709 Nonbonded interactions: 120278 Sorted by model distance: nonbonded pdb=" NH1 ARG B 192 " pdb=" O7 NAG c 1 " model vdw 2.274 3.120 nonbonded pdb=" OH TYR A 60 " pdb=" O PRO A 154 " model vdw 2.298 3.040 nonbonded pdb=" O ALA D 285 " pdb=" OH TYR D 411 " model vdw 2.325 3.040 nonbonded pdb=" O SER F 442 " pdb=" NH2 ARG F 460 " model vdw 2.335 3.120 nonbonded pdb=" NE2 HIS C 107 " pdb=" OG1 THR C 131 " model vdw 2.345 3.120 ... (remaining 120273 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 12 through 66 or resid 68 through 418)) selection = (chain 'D' and (resid 12 through 66 or resid 68 through 418)) } ncs_group { reference = (chain 'B' and (resid 8 through 65 or resid 67 through 300 or resid 302 through \ 501)) selection = (chain 'C' and (resid 8 through 65 or resid 67 through 300 or resid 302 through \ 501)) selection = (chain 'E' and (resid 8 through 65 or resid 67 through 300 or resid 302 through \ 501)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.340 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 : 0.003 0.033 15386 Z= 0.146 Angle : 0.499 5.630 20975 Z= 0.232 Chirality : 0.042 0.241 2435 Planarity : 0.003 0.044 2550 Dihedral : 11.632 105.765 6015 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.50 % Allowed : 2.96 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.20), residues: 1774 helix: 0.60 (0.21), residues: 559 sheet: 0.36 (0.23), residues: 493 loop : 0.30 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 136 TYR 0.012 0.001 TYR C 277 PHE 0.007 0.001 PHE A 157 TRP 0.005 0.001 TRP C 67 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00311 (15349) covalent geometry : angle 0.49158 (20870) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.38328 ( 12) hydrogen bonds : bond 0.25139 ( 719) hydrogen bonds : angle 7.51283 ( 2366) link_ALPHA1-3 : bond 0.00240 ( 5) link_ALPHA1-3 : angle 1.15966 ( 15) link_ALPHA1-6 : bond 0.00422 ( 5) link_ALPHA1-6 : angle 0.91653 ( 15) link_BETA1-4 : bond 0.00439 ( 13) link_BETA1-4 : angle 1.59264 ( 39) link_NAG-ASN : bond 0.00282 ( 8) link_NAG-ASN : angle 1.39058 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 266 MET cc_start: 0.9134 (mmm) cc_final: 0.8872 (mmm) REVERT: E 190 GLU cc_start: 0.8623 (tt0) cc_final: 0.8406 (tt0) REVERT: B 9 MET cc_start: 0.9139 (mtp) cc_final: 0.8847 (mtp) REVERT: A 282 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7722 (p90) REVERT: C 61 MET cc_start: 0.9321 (ptt) cc_final: 0.9115 (ptt) REVERT: C 215 LYS cc_start: 0.8915 (tttt) cc_final: 0.8617 (tttp) REVERT: C 275 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9099 (pp) REVERT: C 309 GLN cc_start: 0.8292 (mt0) cc_final: 0.7966 (mp10) REVERT: F 426 ARG cc_start: 0.8986 (ptt180) cc_final: 0.8770 (ptp90) REVERT: F 464 LYS cc_start: 0.8288 (pttm) cc_final: 0.7942 (tmmt) REVERT: F 475 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8767 (ptmm) REVERT: F 481 VAL cc_start: 0.8820 (t) cc_final: 0.8595 (p) REVERT: F 491 SER cc_start: 0.8832 (m) cc_final: 0.8621 (m) outliers start: 8 outliers final: 4 residues processed: 209 average time/residue: 0.8353 time to fit residues: 187.5545 Evaluate side-chains 149 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 GLN E 90 GLN E 185 GLN E 243 ASN B 41 ASN B 243 ASN B 303 ASN A 56 HIS A 229 GLN A 248 ASN C 90 GLN C 224 GLN C 303 ASN F 427 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.052675 restraints weight = 58169.113| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.12 r_work: 0.2444 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2450 r_free = 0.2450 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2449 r_free = 0.2449 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15386 Z= 0.135 Angle : 0.562 7.685 20975 Z= 0.294 Chirality : 0.043 0.194 2435 Planarity : 0.004 0.047 2550 Dihedral : 10.367 80.756 2663 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.45 % Allowed : 8.07 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1774 helix: 1.79 (0.20), residues: 600 sheet: 0.50 (0.24), residues: 447 loop : 0.40 (0.25), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 425 TYR 0.018 0.001 TYR B 299 PHE 0.013 0.001 PHE A 298 TRP 0.010 0.001 TRP C 67 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00288 (15349) covalent geometry : angle 0.55195 (20870) SS BOND : bond 0.00133 ( 6) SS BOND : angle 0.48804 ( 12) hydrogen bonds : bond 0.05717 ( 719) hydrogen bonds : angle 4.86643 ( 2366) link_ALPHA1-3 : bond 0.00943 ( 5) link_ALPHA1-3 : angle 2.01174 ( 15) link_ALPHA1-6 : bond 0.00798 ( 5) link_ALPHA1-6 : angle 2.13702 ( 15) link_BETA1-4 : bond 0.00512 ( 13) link_BETA1-4 : angle 1.62020 ( 39) link_NAG-ASN : bond 0.00323 ( 8) link_NAG-ASN : angle 1.23812 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: D 63 ASP cc_start: 0.8712 (m-30) cc_final: 0.8204 (m-30) REVERT: E 141 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8470 (mtp85) REVERT: E 261 MET cc_start: 0.9173 (tpt) cc_final: 0.8899 (mmt) REVERT: E 270 GLU cc_start: 0.8927 (tt0) cc_final: 0.8186 (tm-30) REVERT: E 309 GLN cc_start: 0.7175 (mt0) cc_final: 0.6867 (mt0) REVERT: B 9 MET cc_start: 0.8959 (mtp) cc_final: 0.8534 (mtp) REVERT: B 225 THR cc_start: 0.9438 (m) cc_final: 0.9038 (p) REVERT: B 309 GLN cc_start: 0.7404 (mt0) cc_final: 0.7013 (mp-120) REVERT: A 277 LEU cc_start: 0.8941 (tt) cc_final: 0.8688 (tt) REVERT: A 282 TYR cc_start: 0.8022 (p90) cc_final: 0.7433 (p90) REVERT: C 70 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9089 (mmtp) REVERT: F 426 ARG cc_start: 0.8596 (ptt180) cc_final: 0.8228 (ptt180) REVERT: F 434 GLU cc_start: 0.8629 (tt0) cc_final: 0.8154 (pt0) REVERT: F 448 TYR cc_start: 0.8733 (m-80) cc_final: 0.8491 (m-80) REVERT: F 450 ASP cc_start: 0.9178 (m-30) cc_final: 0.8968 (m-30) REVERT: F 453 LYS cc_start: 0.8569 (ptpp) cc_final: 0.8367 (ptpp) REVERT: F 464 LYS cc_start: 0.8932 (pttm) cc_final: 0.8652 (ptmm) REVERT: F 475 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8576 (ttpp) REVERT: F 478 ASP cc_start: 0.8771 (m-30) cc_final: 0.8515 (m-30) REVERT: F 481 VAL cc_start: 0.8193 (t) cc_final: 0.7828 (p) REVERT: F 491 SER cc_start: 0.9197 (m) cc_final: 0.8751 (m) outliers start: 23 outliers final: 8 residues processed: 162 average time/residue: 0.7612 time to fit residues: 133.7724 Evaluate side-chains 151 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 172 optimal weight: 0.0040 chunk 85 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 155 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 151 HIS D 242 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN A 229 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.052412 restraints weight = 63284.033| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 4.25 r_work: 0.2431 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15386 Z= 0.136 Angle : 0.526 8.802 20975 Z= 0.272 Chirality : 0.043 0.219 2435 Planarity : 0.004 0.054 2550 Dihedral : 9.530 74.263 2661 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.20 % Allowed : 8.95 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.20), residues: 1774 helix: 2.16 (0.21), residues: 600 sheet: 0.47 (0.23), residues: 465 loop : 0.34 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 407 TYR 0.022 0.001 TYR E 299 PHE 0.012 0.001 PHE A 304 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00310 (15349) covalent geometry : angle 0.51639 (20870) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.38549 ( 12) hydrogen bonds : bond 0.04793 ( 719) hydrogen bonds : angle 4.39293 ( 2366) link_ALPHA1-3 : bond 0.01015 ( 5) link_ALPHA1-3 : angle 1.79040 ( 15) link_ALPHA1-6 : bond 0.00706 ( 5) link_ALPHA1-6 : angle 1.97996 ( 15) link_BETA1-4 : bond 0.00433 ( 13) link_BETA1-4 : angle 1.47138 ( 39) link_NAG-ASN : bond 0.00172 ( 8) link_NAG-ASN : angle 1.26007 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: D 63 ASP cc_start: 0.8695 (m-30) cc_final: 0.8309 (m-30) REVERT: E 141 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8530 (mtp85) REVERT: E 200 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7174 (t80) REVERT: E 227 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7748 (ttt) REVERT: E 261 MET cc_start: 0.9188 (tpt) cc_final: 0.8912 (mmt) REVERT: E 270 GLU cc_start: 0.9015 (tt0) cc_final: 0.8377 (tm-30) REVERT: B 9 MET cc_start: 0.8964 (mtp) cc_final: 0.8418 (mtp) REVERT: B 61 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.9254 (ptt) REVERT: B 185 GLN cc_start: 0.8609 (pm20) cc_final: 0.8367 (pm20) REVERT: B 225 THR cc_start: 0.9430 (m) cc_final: 0.9099 (p) REVERT: B 309 GLN cc_start: 0.7399 (mt0) cc_final: 0.7138 (mp-120) REVERT: A 282 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7324 (p90) REVERT: F 426 ARG cc_start: 0.8611 (ptt180) cc_final: 0.8116 (ptt180) REVERT: F 434 GLU cc_start: 0.8651 (tt0) cc_final: 0.8012 (pt0) REVERT: F 448 TYR cc_start: 0.8805 (m-80) cc_final: 0.8517 (m-80) REVERT: F 450 ASP cc_start: 0.9159 (m-30) cc_final: 0.8917 (m-30) REVERT: F 464 LYS cc_start: 0.8969 (pttm) cc_final: 0.8686 (ptmm) REVERT: F 475 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8602 (ttpp) REVERT: F 478 ASP cc_start: 0.8699 (m-30) cc_final: 0.8465 (m-30) REVERT: F 481 VAL cc_start: 0.8287 (t) cc_final: 0.7879 (p) REVERT: F 491 SER cc_start: 0.9235 (m) cc_final: 0.8799 (m) outliers start: 19 outliers final: 11 residues processed: 152 average time/residue: 0.7425 time to fit residues: 122.7560 Evaluate side-chains 153 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 0.0570 chunk 106 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN A 229 GLN C 224 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.051221 restraints weight = 58149.496| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 4.10 r_work: 0.2409 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2418 r_free = 0.2418 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15386 Z= 0.200 Angle : 0.558 7.569 20975 Z= 0.285 Chirality : 0.044 0.233 2435 Planarity : 0.004 0.054 2550 Dihedral : 9.154 70.850 2660 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.83 % Allowed : 9.14 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.20), residues: 1774 helix: 2.27 (0.21), residues: 600 sheet: 0.42 (0.23), residues: 463 loop : 0.25 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 407 TYR 0.023 0.002 TYR E 299 PHE 0.015 0.001 PHE A 298 TRP 0.009 0.001 TRP C 67 HIS 0.002 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00471 (15349) covalent geometry : angle 0.54788 (20870) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.39625 ( 12) hydrogen bonds : bond 0.04718 ( 719) hydrogen bonds : angle 4.32928 ( 2366) link_ALPHA1-3 : bond 0.01038 ( 5) link_ALPHA1-3 : angle 2.02506 ( 15) link_ALPHA1-6 : bond 0.00700 ( 5) link_ALPHA1-6 : angle 2.06874 ( 15) link_BETA1-4 : bond 0.00356 ( 13) link_BETA1-4 : angle 1.50227 ( 39) link_NAG-ASN : bond 0.00202 ( 8) link_NAG-ASN : angle 1.40001 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 58 MET cc_start: 0.8926 (mtp) cc_final: 0.8304 (tpt) REVERT: D 63 ASP cc_start: 0.8673 (m-30) cc_final: 0.8289 (m-30) REVERT: D 141 MET cc_start: 0.9047 (mtt) cc_final: 0.8784 (mtp) REVERT: E 141 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8547 (mtp85) REVERT: E 200 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7169 (t80) REVERT: E 261 MET cc_start: 0.9151 (tpt) cc_final: 0.8896 (mmt) REVERT: E 270 GLU cc_start: 0.9075 (tt0) cc_final: 0.8389 (tm-30) REVERT: E 309 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7078 (mt0) REVERT: B 9 MET cc_start: 0.8952 (mtp) cc_final: 0.8709 (mtm) REVERT: B 61 MET cc_start: 0.9550 (OUTLIER) cc_final: 0.9240 (ptt) REVERT: B 185 GLN cc_start: 0.8728 (pm20) cc_final: 0.8392 (pm20) REVERT: B 225 THR cc_start: 0.9439 (m) cc_final: 0.9144 (p) REVERT: B 227 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8119 (ttt) REVERT: B 309 GLN cc_start: 0.7447 (mt0) cc_final: 0.7164 (mp-120) REVERT: A 204 GLN cc_start: 0.8988 (tt0) cc_final: 0.8260 (tt0) REVERT: A 282 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7247 (p90) REVERT: C 70 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9050 (mmtp) REVERT: F 4 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8234 (mp10) REVERT: F 426 ARG cc_start: 0.8584 (ptt180) cc_final: 0.8082 (ptt180) REVERT: F 434 GLU cc_start: 0.8662 (tt0) cc_final: 0.7998 (pt0) REVERT: F 448 TYR cc_start: 0.8777 (m-80) cc_final: 0.8386 (m-80) REVERT: F 464 LYS cc_start: 0.9017 (pttm) cc_final: 0.8748 (ptmm) REVERT: F 475 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8568 (ttpp) REVERT: F 478 ASP cc_start: 0.8676 (m-30) cc_final: 0.8456 (m-30) REVERT: F 481 VAL cc_start: 0.8294 (t) cc_final: 0.7870 (p) REVERT: F 483 TYR cc_start: 0.7771 (m-80) cc_final: 0.7378 (m-80) REVERT: F 491 SER cc_start: 0.9288 (m) cc_final: 0.8811 (m) outliers start: 29 outliers final: 12 residues processed: 159 average time/residue: 0.7033 time to fit residues: 122.2567 Evaluate side-chains 159 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain F residue 466 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 29 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN F 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.051931 restraints weight = 75849.607| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 4.60 r_work: 0.2410 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2419 r_free = 0.2419 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15386 Z= 0.119 Angle : 0.525 8.721 20975 Z= 0.266 Chirality : 0.043 0.240 2435 Planarity : 0.003 0.050 2550 Dihedral : 8.499 66.934 2658 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.64 % Allowed : 9.71 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1774 helix: 2.38 (0.21), residues: 602 sheet: 0.48 (0.23), residues: 463 loop : 0.30 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 407 TYR 0.023 0.001 TYR E 299 PHE 0.012 0.001 PHE D 157 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.000 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00268 (15349) covalent geometry : angle 0.51492 (20870) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.29939 ( 12) hydrogen bonds : bond 0.04131 ( 719) hydrogen bonds : angle 4.08302 ( 2366) link_ALPHA1-3 : bond 0.01146 ( 5) link_ALPHA1-3 : angle 1.99438 ( 15) link_ALPHA1-6 : bond 0.00828 ( 5) link_ALPHA1-6 : angle 2.04255 ( 15) link_BETA1-4 : bond 0.00349 ( 13) link_BETA1-4 : angle 1.39407 ( 39) link_NAG-ASN : bond 0.00145 ( 8) link_NAG-ASN : angle 1.26146 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.725 Fit side-chains REVERT: D 58 MET cc_start: 0.8846 (mtp) cc_final: 0.8292 (tpt) REVERT: D 63 ASP cc_start: 0.8696 (m-30) cc_final: 0.8369 (m-30) REVERT: D 112 MET cc_start: 0.8659 (tpp) cc_final: 0.8447 (ttp) REVERT: D 141 MET cc_start: 0.9004 (mtt) cc_final: 0.8775 (mtp) REVERT: E 141 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8570 (mtp85) REVERT: E 270 GLU cc_start: 0.9061 (tt0) cc_final: 0.8484 (tm-30) REVERT: E 309 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6676 (mt0) REVERT: B 9 MET cc_start: 0.8969 (mtp) cc_final: 0.8727 (mtm) REVERT: B 141 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8155 (mtp85) REVERT: B 185 GLN cc_start: 0.8800 (pm20) cc_final: 0.8411 (pm20) REVERT: B 225 THR cc_start: 0.9421 (m) cc_final: 0.9176 (p) REVERT: B 227 MET cc_start: 0.8497 (ttm) cc_final: 0.8070 (ttt) REVERT: B 309 GLN cc_start: 0.7292 (mt0) cc_final: 0.6978 (mp-120) REVERT: A 58 MET cc_start: 0.8859 (mtm) cc_final: 0.8515 (mtp) REVERT: A 204 GLN cc_start: 0.9010 (tt0) cc_final: 0.8274 (tt0) REVERT: A 277 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 282 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7250 (p90) REVERT: C 70 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9104 (mmtp) REVERT: C 141 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8548 (mpp80) REVERT: F 426 ARG cc_start: 0.8569 (ptt180) cc_final: 0.7938 (ptt180) REVERT: F 434 GLU cc_start: 0.8693 (tt0) cc_final: 0.7961 (pt0) REVERT: F 448 TYR cc_start: 0.8822 (m-80) cc_final: 0.8423 (m-80) REVERT: F 450 ASP cc_start: 0.9246 (t70) cc_final: 0.9009 (m-30) REVERT: F 464 LYS cc_start: 0.9030 (pttm) cc_final: 0.8734 (ptmm) REVERT: F 475 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8651 (ttpp) REVERT: F 478 ASP cc_start: 0.8536 (m-30) cc_final: 0.8311 (m-30) REVERT: F 481 VAL cc_start: 0.8312 (t) cc_final: 0.7888 (p) REVERT: F 483 TYR cc_start: 0.7802 (m-80) cc_final: 0.7410 (m-80) REVERT: F 491 SER cc_start: 0.9237 (m) cc_final: 0.8798 (m) outliers start: 26 outliers final: 11 residues processed: 160 average time/residue: 0.7526 time to fit residues: 131.2010 Evaluate side-chains 156 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 447 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 53 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 35 optimal weight: 0.0040 chunk 167 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN F 4 GLN F 415 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.052347 restraints weight = 65369.835| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 4.31 r_work: 0.2429 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15386 Z= 0.127 Angle : 0.525 9.741 20975 Z= 0.267 Chirality : 0.043 0.245 2435 Planarity : 0.003 0.045 2550 Dihedral : 8.156 64.735 2658 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.77 % Allowed : 9.65 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1774 helix: 2.39 (0.20), residues: 609 sheet: 0.47 (0.23), residues: 453 loop : 0.28 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 407 TYR 0.023 0.001 TYR E 299 PHE 0.012 0.001 PHE A 304 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.000 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00291 (15349) covalent geometry : angle 0.51491 (20870) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.25845 ( 12) hydrogen bonds : bond 0.04012 ( 719) hydrogen bonds : angle 4.01845 ( 2366) link_ALPHA1-3 : bond 0.01145 ( 5) link_ALPHA1-3 : angle 2.04217 ( 15) link_ALPHA1-6 : bond 0.00868 ( 5) link_ALPHA1-6 : angle 2.03341 ( 15) link_BETA1-4 : bond 0.00366 ( 13) link_BETA1-4 : angle 1.37901 ( 39) link_NAG-ASN : bond 0.00127 ( 8) link_NAG-ASN : angle 1.30986 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.575 Fit side-chains REVERT: D 63 ASP cc_start: 0.8665 (m-30) cc_final: 0.8326 (m-30) REVERT: D 112 MET cc_start: 0.8711 (tpp) cc_final: 0.8465 (ttp) REVERT: D 141 MET cc_start: 0.9031 (mtt) cc_final: 0.8731 (mtp) REVERT: E 141 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8567 (mtp85) REVERT: E 200 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7125 (t80) REVERT: E 270 GLU cc_start: 0.9058 (tt0) cc_final: 0.8488 (tm-30) REVERT: E 309 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6531 (mp-120) REVERT: B 9 MET cc_start: 0.8920 (mtp) cc_final: 0.8672 (mtm) REVERT: B 141 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8137 (mtp85) REVERT: B 185 GLN cc_start: 0.8807 (pm20) cc_final: 0.8373 (pm20) REVERT: B 225 THR cc_start: 0.9404 (m) cc_final: 0.9171 (p) REVERT: B 227 MET cc_start: 0.8508 (ttm) cc_final: 0.8094 (ttt) REVERT: B 309 GLN cc_start: 0.7357 (mt0) cc_final: 0.7150 (mp-120) REVERT: A 58 MET cc_start: 0.8860 (mtm) cc_final: 0.8621 (mtp) REVERT: A 204 GLN cc_start: 0.9003 (tt0) cc_final: 0.8319 (tt0) REVERT: A 282 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7139 (p90) REVERT: C 70 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9092 (mmtp) REVERT: C 141 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8530 (mpp80) REVERT: F 4 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8380 (mm110) REVERT: F 434 GLU cc_start: 0.8654 (tt0) cc_final: 0.8349 (tt0) REVERT: F 448 TYR cc_start: 0.8827 (m-80) cc_final: 0.8418 (m-80) REVERT: F 450 ASP cc_start: 0.9215 (t70) cc_final: 0.9010 (m-30) REVERT: F 464 LYS cc_start: 0.8941 (pttm) cc_final: 0.8702 (ptmm) REVERT: F 475 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8653 (ttpp) REVERT: F 478 ASP cc_start: 0.8508 (m-30) cc_final: 0.8287 (m-30) REVERT: F 481 VAL cc_start: 0.8291 (t) cc_final: 0.7865 (p) REVERT: F 491 SER cc_start: 0.9200 (m) cc_final: 0.8733 (m) outliers start: 28 outliers final: 13 residues processed: 155 average time/residue: 0.7909 time to fit residues: 133.0286 Evaluate side-chains 158 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 4 GLN Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 466 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 135 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 142 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN F 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.073877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.053276 restraints weight = 51688.064| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.90 r_work: 0.2466 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15386 Z= 0.110 Angle : 0.535 10.439 20975 Z= 0.267 Chirality : 0.043 0.245 2435 Planarity : 0.003 0.067 2550 Dihedral : 7.861 62.809 2658 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.58 % Allowed : 10.53 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.20), residues: 1774 helix: 2.45 (0.20), residues: 609 sheet: 0.48 (0.23), residues: 453 loop : 0.31 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 407 TYR 0.023 0.001 TYR E 299 PHE 0.012 0.001 PHE D 157 TRP 0.011 0.001 TRP C 67 HIS 0.002 0.000 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00247 (15349) covalent geometry : angle 0.52548 (20870) SS BOND : bond 0.00132 ( 6) SS BOND : angle 0.24712 ( 12) hydrogen bonds : bond 0.03822 ( 719) hydrogen bonds : angle 3.93823 ( 2366) link_ALPHA1-3 : bond 0.01143 ( 5) link_ALPHA1-3 : angle 2.01982 ( 15) link_ALPHA1-6 : bond 0.00895 ( 5) link_ALPHA1-6 : angle 1.99468 ( 15) link_BETA1-4 : bond 0.00386 ( 13) link_BETA1-4 : angle 1.35682 ( 39) link_NAG-ASN : bond 0.00134 ( 8) link_NAG-ASN : angle 1.27141 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: D 63 ASP cc_start: 0.8624 (m-30) cc_final: 0.8287 (m-30) REVERT: D 112 MET cc_start: 0.8759 (tpp) cc_final: 0.8557 (ttp) REVERT: E 141 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8544 (mtp85) REVERT: E 200 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7152 (t80) REVERT: E 227 MET cc_start: 0.7960 (ttt) cc_final: 0.7744 (ttt) REVERT: E 270 GLU cc_start: 0.9055 (tt0) cc_final: 0.8492 (tm-30) REVERT: E 309 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6683 (mp-120) REVERT: B 9 MET cc_start: 0.8943 (mtp) cc_final: 0.8697 (mtm) REVERT: B 141 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8108 (mtp85) REVERT: B 185 GLN cc_start: 0.8848 (pm20) cc_final: 0.8391 (pm20) REVERT: B 225 THR cc_start: 0.9398 (m) cc_final: 0.9197 (p) REVERT: B 227 MET cc_start: 0.8465 (ttm) cc_final: 0.8044 (ttt) REVERT: A 58 MET cc_start: 0.8858 (mtm) cc_final: 0.8616 (mtp) REVERT: A 204 GLN cc_start: 0.8987 (tt0) cc_final: 0.8387 (tt0) REVERT: A 282 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7260 (p90) REVERT: C 70 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9089 (mmtp) REVERT: C 141 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8523 (mpp80) REVERT: F 434 GLU cc_start: 0.8697 (tt0) cc_final: 0.8129 (pt0) REVERT: F 448 TYR cc_start: 0.8829 (m-80) cc_final: 0.8396 (m-80) REVERT: F 464 LYS cc_start: 0.8934 (pttm) cc_final: 0.8708 (ptmm) REVERT: F 475 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8658 (ttpp) REVERT: F 481 VAL cc_start: 0.8247 (t) cc_final: 0.7915 (p) REVERT: F 491 SER cc_start: 0.9211 (m) cc_final: 0.8767 (m) outliers start: 25 outliers final: 11 residues processed: 154 average time/residue: 0.8030 time to fit residues: 133.9273 Evaluate side-chains 157 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 466 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN A 229 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.074670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.053367 restraints weight = 75243.111| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 4.59 r_work: 0.2447 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15386 Z= 0.099 Angle : 0.527 11.535 20975 Z= 0.265 Chirality : 0.043 0.241 2435 Planarity : 0.003 0.044 2550 Dihedral : 7.400 59.724 2658 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.32 % Allowed : 10.78 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.20), residues: 1774 helix: 2.51 (0.20), residues: 609 sheet: 0.55 (0.23), residues: 453 loop : 0.34 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 407 TYR 0.022 0.001 TYR E 299 PHE 0.013 0.001 PHE D 157 TRP 0.017 0.001 TRP F 441 HIS 0.002 0.000 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00217 (15349) covalent geometry : angle 0.51855 (20870) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.25978 ( 12) hydrogen bonds : bond 0.03542 ( 719) hydrogen bonds : angle 3.83386 ( 2366) link_ALPHA1-3 : bond 0.01176 ( 5) link_ALPHA1-3 : angle 2.01645 ( 15) link_ALPHA1-6 : bond 0.00943 ( 5) link_ALPHA1-6 : angle 1.93758 ( 15) link_BETA1-4 : bond 0.00406 ( 13) link_BETA1-4 : angle 1.32354 ( 39) link_NAG-ASN : bond 0.00154 ( 8) link_NAG-ASN : angle 1.25039 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.610 Fit side-chains REVERT: D 63 ASP cc_start: 0.8675 (m-30) cc_final: 0.8347 (m-30) REVERT: D 112 MET cc_start: 0.8823 (tpp) cc_final: 0.8593 (ttp) REVERT: E 9 MET cc_start: 0.8196 (mtp) cc_final: 0.7905 (tpp) REVERT: E 64 GLN cc_start: 0.9031 (mp10) cc_final: 0.8403 (mp10) REVERT: E 141 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8550 (mtp85) REVERT: E 200 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7129 (t80) REVERT: E 224 GLN cc_start: 0.8746 (tp40) cc_final: 0.8234 (tp40) REVERT: E 227 MET cc_start: 0.7947 (ttt) cc_final: 0.7739 (ttt) REVERT: E 270 GLU cc_start: 0.9089 (tt0) cc_final: 0.8640 (tm-30) REVERT: E 309 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6550 (mp-120) REVERT: B 9 MET cc_start: 0.8928 (mtp) cc_final: 0.8682 (mtm) REVERT: B 141 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8153 (mtp85) REVERT: B 185 GLN cc_start: 0.8892 (pm20) cc_final: 0.8410 (pm20) REVERT: B 227 MET cc_start: 0.8329 (ttm) cc_final: 0.7916 (ttt) REVERT: A 58 MET cc_start: 0.8860 (mtm) cc_final: 0.8648 (mtp) REVERT: A 204 GLN cc_start: 0.9014 (tt0) cc_final: 0.8318 (tt0) REVERT: A 274 ARG cc_start: 0.8631 (tpt90) cc_final: 0.8427 (tpt90) REVERT: A 282 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7295 (p90) REVERT: C 70 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9116 (mmtp) REVERT: C 141 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8569 (mpp80) REVERT: F 434 GLU cc_start: 0.8792 (tt0) cc_final: 0.8165 (pt0) REVERT: F 448 TYR cc_start: 0.8948 (m-80) cc_final: 0.8554 (m-80) REVERT: F 457 THR cc_start: 0.9051 (m) cc_final: 0.8648 (t) REVERT: F 464 LYS cc_start: 0.8943 (pttm) cc_final: 0.8704 (ptmm) REVERT: F 475 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8597 (ttpp) REVERT: F 478 ASP cc_start: 0.8372 (m-30) cc_final: 0.8080 (m-30) REVERT: F 481 VAL cc_start: 0.8189 (t) cc_final: 0.7859 (p) REVERT: F 491 SER cc_start: 0.9188 (m) cc_final: 0.8775 (m) outliers start: 21 outliers final: 9 residues processed: 153 average time/residue: 0.7893 time to fit residues: 131.0468 Evaluate side-chains 150 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 466 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.074896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.053951 restraints weight = 60998.122| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 4.22 r_work: 0.2470 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15386 Z= 0.103 Angle : 0.540 11.921 20975 Z= 0.268 Chirality : 0.043 0.242 2435 Planarity : 0.003 0.047 2550 Dihedral : 7.059 57.471 2657 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.01 % Allowed : 11.41 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.20), residues: 1774 helix: 2.53 (0.20), residues: 609 sheet: 0.58 (0.23), residues: 453 loop : 0.35 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 407 TYR 0.022 0.001 TYR E 299 PHE 0.011 0.001 PHE D 157 TRP 0.019 0.001 TRP F 441 HIS 0.002 0.000 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00230 (15349) covalent geometry : angle 0.53139 (20870) SS BOND : bond 0.00134 ( 6) SS BOND : angle 0.23146 ( 12) hydrogen bonds : bond 0.03475 ( 719) hydrogen bonds : angle 3.79669 ( 2366) link_ALPHA1-3 : bond 0.01131 ( 5) link_ALPHA1-3 : angle 1.99531 ( 15) link_ALPHA1-6 : bond 0.00952 ( 5) link_ALPHA1-6 : angle 1.85133 ( 15) link_BETA1-4 : bond 0.00404 ( 13) link_BETA1-4 : angle 1.33398 ( 39) link_NAG-ASN : bond 0.00139 ( 8) link_NAG-ASN : angle 1.29032 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.620 Fit side-chains REVERT: D 63 ASP cc_start: 0.8659 (m-30) cc_final: 0.8328 (m-30) REVERT: E 9 MET cc_start: 0.8186 (mtp) cc_final: 0.7851 (tpp) REVERT: E 64 GLN cc_start: 0.9053 (mp10) cc_final: 0.8438 (mp10) REVERT: E 141 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8555 (mtp85) REVERT: E 200 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.7118 (t80) REVERT: E 224 GLN cc_start: 0.8756 (tp40) cc_final: 0.8184 (tp-100) REVERT: E 270 GLU cc_start: 0.9099 (tt0) cc_final: 0.8646 (tm-30) REVERT: E 309 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6573 (mp-120) REVERT: B 9 MET cc_start: 0.8929 (mtp) cc_final: 0.8684 (mtm) REVERT: B 141 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8133 (mtp85) REVERT: B 185 GLN cc_start: 0.8902 (pm20) cc_final: 0.8402 (pm20) REVERT: B 227 MET cc_start: 0.8330 (ttm) cc_final: 0.7912 (ttt) REVERT: A 58 MET cc_start: 0.8865 (mtm) cc_final: 0.8653 (mtp) REVERT: A 204 GLN cc_start: 0.9013 (tt0) cc_final: 0.8319 (tt0) REVERT: A 282 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7328 (p90) REVERT: C 70 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9111 (mmtp) REVERT: F 434 GLU cc_start: 0.8856 (tt0) cc_final: 0.8301 (pt0) REVERT: F 448 TYR cc_start: 0.8949 (m-80) cc_final: 0.8551 (m-80) REVERT: F 457 THR cc_start: 0.9022 (m) cc_final: 0.8716 (t) REVERT: F 460 ARG cc_start: 0.8024 (pmt170) cc_final: 0.7530 (ptt-90) REVERT: F 464 LYS cc_start: 0.8937 (pttm) cc_final: 0.8719 (ptmm) REVERT: F 475 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8588 (ttpp) REVERT: F 478 ASP cc_start: 0.8334 (m-30) cc_final: 0.8125 (m-30) REVERT: F 481 VAL cc_start: 0.8226 (t) cc_final: 0.7920 (p) REVERT: F 491 SER cc_start: 0.9131 (m) cc_final: 0.8700 (m) outliers start: 16 outliers final: 8 residues processed: 148 average time/residue: 0.8022 time to fit residues: 128.7216 Evaluate side-chains 146 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 466 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 94 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 50 optimal weight: 0.0040 chunk 140 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 overall best weight: 0.5654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN A 229 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.075492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.054158 restraints weight = 75555.134| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 4.61 r_work: 0.2459 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15386 Z= 0.104 Angle : 0.549 12.483 20975 Z= 0.277 Chirality : 0.042 0.242 2435 Planarity : 0.003 0.048 2550 Dihedral : 6.847 55.849 2657 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.95 % Allowed : 11.54 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.20), residues: 1774 helix: 2.55 (0.20), residues: 609 sheet: 0.63 (0.23), residues: 453 loop : 0.37 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 312 TYR 0.025 0.001 TYR E 299 PHE 0.012 0.001 PHE D 157 TRP 0.015 0.001 TRP F 441 HIS 0.002 0.000 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00228 (15349) covalent geometry : angle 0.54149 (20870) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.25846 ( 12) hydrogen bonds : bond 0.03428 ( 719) hydrogen bonds : angle 3.80400 ( 2366) link_ALPHA1-3 : bond 0.01108 ( 5) link_ALPHA1-3 : angle 1.94010 ( 15) link_ALPHA1-6 : bond 0.00945 ( 5) link_ALPHA1-6 : angle 1.71108 ( 15) link_BETA1-4 : bond 0.00426 ( 13) link_BETA1-4 : angle 1.34197 ( 39) link_NAG-ASN : bond 0.00148 ( 8) link_NAG-ASN : angle 1.28216 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.672 Fit side-chains REVERT: D 58 MET cc_start: 0.8762 (mtp) cc_final: 0.8221 (tpt) REVERT: D 63 ASP cc_start: 0.8686 (m-30) cc_final: 0.8356 (m-30) REVERT: E 64 GLN cc_start: 0.9044 (mp10) cc_final: 0.8472 (mp10) REVERT: E 141 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8577 (mtp85) REVERT: E 182 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8607 (pm20) REVERT: E 224 GLN cc_start: 0.8716 (tp40) cc_final: 0.8127 (tp40) REVERT: E 270 GLU cc_start: 0.9107 (tt0) cc_final: 0.8665 (tm-30) REVERT: E 309 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6543 (mp-120) REVERT: B 9 MET cc_start: 0.8921 (mtp) cc_final: 0.8679 (mtm) REVERT: B 141 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8142 (mtp85) REVERT: B 185 GLN cc_start: 0.8907 (pm20) cc_final: 0.8409 (pm20) REVERT: B 227 MET cc_start: 0.8326 (ttm) cc_final: 0.7947 (ttt) REVERT: A 204 GLN cc_start: 0.9002 (tt0) cc_final: 0.8531 (tt0) REVERT: A 282 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7298 (p90) REVERT: C 70 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9126 (mmtp) REVERT: F 434 GLU cc_start: 0.8869 (tt0) cc_final: 0.8333 (pt0) REVERT: F 448 TYR cc_start: 0.8976 (m-80) cc_final: 0.8551 (m-80) REVERT: F 460 ARG cc_start: 0.7980 (pmt170) cc_final: 0.7580 (ptt-90) REVERT: F 464 LYS cc_start: 0.8896 (pttm) cc_final: 0.8674 (ptmm) REVERT: F 475 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8565 (ttpp) REVERT: F 478 ASP cc_start: 0.8345 (m-30) cc_final: 0.8094 (m-30) REVERT: F 481 VAL cc_start: 0.8229 (t) cc_final: 0.7919 (p) REVERT: F 491 SER cc_start: 0.9125 (m) cc_final: 0.8708 (m) outliers start: 15 outliers final: 7 residues processed: 141 average time/residue: 0.8221 time to fit residues: 125.4554 Evaluate side-chains 141 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain F residue 466 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 80 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.052943 restraints weight = 48139.919| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.78 r_work: 0.2463 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15386 Z= 0.165 Angle : 0.583 12.356 20975 Z= 0.294 Chirality : 0.044 0.237 2435 Planarity : 0.003 0.049 2550 Dihedral : 6.628 57.972 2657 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.07 % Allowed : 11.79 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.20), residues: 1774 helix: 2.53 (0.21), residues: 609 sheet: 0.50 (0.23), residues: 453 loop : 0.28 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 407 TYR 0.024 0.001 TYR E 299 PHE 0.014 0.001 PHE A 304 TRP 0.034 0.001 TRP F 441 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00389 (15349) covalent geometry : angle 0.57429 (20870) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.34925 ( 12) hydrogen bonds : bond 0.03980 ( 719) hydrogen bonds : angle 3.96378 ( 2366) link_ALPHA1-3 : bond 0.01011 ( 5) link_ALPHA1-3 : angle 2.01795 ( 15) link_ALPHA1-6 : bond 0.00852 ( 5) link_ALPHA1-6 : angle 1.74814 ( 15) link_BETA1-4 : bond 0.00410 ( 13) link_BETA1-4 : angle 1.47778 ( 39) link_NAG-ASN : bond 0.00180 ( 8) link_NAG-ASN : angle 1.46205 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4836.36 seconds wall clock time: 83 minutes 28.12 seconds (5008.12 seconds total)