Starting phenix.real_space_refine on Wed Mar 4 20:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qn9_14071/03_2026/7qn9_14071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn9_14071/03_2026/7qn9_14071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qn9_14071/03_2026/7qn9_14071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn9_14071/03_2026/7qn9_14071.map" model { file = "/net/cci-nas-00/data/ceres_data/7qn9_14071/03_2026/7qn9_14071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn9_14071/03_2026/7qn9_14071.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 10194 2.51 5 N 2533 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15696 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2693 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 315} Chain breaks: 1 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 bond proxies already assigned to first conformer: 2627 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'HSM': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'D10': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N HSM C 501 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM C 501 " occ=0.70 residue: pdb=" N HSM D 502 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM D 502 " occ=0.70 Time building chain proxies: 3.97, per 1000 atoms: 0.25 Number of scatterers: 15696 At special positions: 0 Unit cell: (113.792, 116.48, 129.92, 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 91 16.00 O 2878 8.00 N 2533 7.00 C 10194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " 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 F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG E 501 " - " ASN E 65 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN C 149 " " NAG H 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 807.5 milliseconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 21 sheets defined 37.8% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 106 through 109 removed outlier: 3.527A pdb=" N LYS A 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 106 through 109' Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.620A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.277A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.760A pdb=" N HIS A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 348 Processing helix chain 'A' and resid 516 through 543 removed outlier: 3.682A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.622A pdb=" N SER A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) 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 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 Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.520A pdb=" N SER B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 246 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 279 through 306 Processing helix chain 'B' and resid 420 through 447 removed outlier: 3.507A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 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 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.520A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 246 through 269 Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 279 through 306 Processing helix chain 'C' and resid 420 through 447 removed outlier: 3.507A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 9 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 238 removed outlier: 3.519A pdb=" N SER D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 246 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 279 through 306 Processing helix chain 'D' and resid 420 through 447 removed outlier: 3.509A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 112 through 118 removed outlier: 3.549A pdb=" N PHE E 115 " --> pdb=" O ASP E 112 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.762A pdb=" N GLU E 201 " --> pdb=" O GLU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 Proline residue: E 257 - end of helix removed outlier: 4.262A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 271 " --> pdb=" O VAL E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 301 removed outlier: 3.698A pdb=" N ARG E 298 " --> pdb=" O MET E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 336 removed outlier: 4.026A pdb=" N ASP E 336 " --> pdb=" O HIS E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 451 removed outlier: 3.541A pdb=" N ALA E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Proline residue: E 436 - end of helix Processing helix chain 'L' and resid 449 through 452 Processing helix chain 'L' and resid 495 through 499 Processing helix chain 'M' and resid 449 through 452 Processing helix chain 'M' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.654A pdb=" N PHE A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 79 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.773A pdb=" N SER A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 167 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER A 142 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ARG A 165 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU A 92 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 79 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N GLU A 213 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE A 78 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.272A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.282A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.283A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.282A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 72 through 79 removed outlier: 5.942A pdb=" N VAL E 72 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE E 90 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE E 78 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU E 84 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA E 129 " --> pdb=" O ALA E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 109 through 111 removed outlier: 4.444A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.996A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AC2, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.818A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) 906 hydrogen bonds defined for protein. 2537 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: 2.92 Time building geometry restraints manager: 1.87 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: 4782 1.34 - 1.46: 4108 1.46 - 1.58: 7050 1.58 - 1.69: 0 1.69 - 1.81: 159 Bond restraints: 16099 Sorted by residual: bond pdb=" C1 BMA a 3 " pdb=" C2 BMA a 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 16094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20799 1.28 - 2.55: 808 2.55 - 3.83: 193 3.83 - 5.11: 48 5.11 - 6.39: 24 Bond angle restraints: 21872 Sorted by residual: angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 116.69 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.86e+01 angle pdb=" C HIS B 267 " pdb=" N LEU B 268 " pdb=" CA LEU B 268 " ideal model delta sigma weight residual 120.38 125.22 -4.84 1.37e+00 5.33e-01 1.25e+01 angle pdb=" C HIS D 267 " pdb=" N LEU D 268 " pdb=" CA LEU D 268 " ideal model delta sigma weight residual 120.38 125.20 -4.82 1.37e+00 5.33e-01 1.24e+01 ... (remaining 21867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 9339 21.75 - 43.49: 325 43.49 - 65.24: 35 65.24 - 86.99: 35 86.99 - 108.73: 19 Dihedral angle restraints: 9753 sinusoidal: 4188 harmonic: 5565 Sorted by residual: dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2091 0.058 - 0.116: 374 0.116 - 0.174: 33 0.174 - 0.231: 7 0.231 - 0.289: 5 Chirality restraints: 2510 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.63e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.52e+01 ... (remaining 2507 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.007 2.00e-02 2.50e+03 1.53e-02 4.68e+00 pdb=" CG TYR C 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " -0.007 2.00e-02 2.50e+03 1.53e-02 4.66e+00 pdb=" CG TYR B 157 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 157 " 0.006 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR D 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 157 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR D 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR D 157 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 157 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR D 157 " 0.022 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 417 2.71 - 3.26: 15527 3.26 - 3.81: 26302 3.81 - 4.35: 33906 4.35 - 4.90: 56253 Nonbonded interactions: 132405 Sorted by model distance: nonbonded pdb=" O TRP M 440 " pdb=" NH1 ARG M 459 " model vdw 2.164 3.120 nonbonded pdb=" O TRP L 440 " pdb=" NH1 ARG L 459 " model vdw 2.165 3.120 nonbonded pdb=" OG1 THR E 215 " pdb=" OD1 ASN E 246 " model vdw 2.224 3.040 nonbonded pdb=" O VAL A 290 " pdb=" OG1 THR A 294 " model vdw 2.257 3.040 nonbonded pdb=" O SER A 305 " pdb=" ND1 HIS A 308 " model vdw 2.267 3.120 ... (remaining 132400 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 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'D' and resid 8 through 447) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 1.920 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: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.500 Find NCS groups from input model: 0.280 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:9.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.034 16132 Z= 0.142 Angle : 0.639 6.387 21964 Z= 0.335 Chirality : 0.046 0.289 2510 Planarity : 0.005 0.058 2682 Dihedral : 13.258 108.734 6168 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.48 % Allowed : 3.60 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1863 helix: 0.70 (0.20), residues: 573 sheet: 0.37 (0.24), residues: 453 loop : 0.33 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG D 28 TYR 0.022 0.004 TYR B 157 PHE 0.017 0.001 PHE D 306 TRP 0.014 0.001 TRP L 440 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00309 (16099) covalent geometry : angle 0.63578 (21872) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.68315 ( 14) hydrogen bonds : bond 0.20689 ( 793) hydrogen bonds : angle 7.39515 ( 2537) link_ALPHA1-3 : bond 0.00121 ( 3) link_ALPHA1-3 : angle 0.71485 ( 9) link_ALPHA1-6 : bond 0.00141 ( 3) link_ALPHA1-6 : angle 0.54745 ( 9) link_BETA1-4 : bond 0.00225 ( 11) link_BETA1-4 : angle 1.19642 ( 33) link_NAG-ASN : bond 0.00186 ( 9) link_NAG-ASN : angle 1.55412 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 427 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 TRP cc_start: 0.7080 (m-10) cc_final: 0.6471 (m100) REVERT: B 13 LYS cc_start: 0.9000 (tttt) cc_final: 0.8686 (ttpp) REVERT: B 215 LYS cc_start: 0.9016 (tttt) cc_final: 0.8781 (ttmm) REVERT: B 298 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8568 (tm-30) REVERT: B 306 PHE cc_start: 0.7427 (t80) cc_final: 0.7067 (t80) REVERT: C 9 MET cc_start: 0.8505 (mtp) cc_final: 0.8185 (mtt) REVERT: C 90 GLN cc_start: 0.8970 (mp10) cc_final: 0.8271 (mp10) REVERT: C 230 ILE cc_start: 0.9663 (mt) cc_final: 0.9431 (mp) REVERT: D 13 LYS cc_start: 0.9103 (tttt) cc_final: 0.8671 (tmmt) REVERT: D 190 GLU cc_start: 0.8018 (tt0) cc_final: 0.7741 (tt0) REVERT: D 214 LEU cc_start: 0.8965 (mt) cc_final: 0.8748 (mt) REVERT: D 215 LYS cc_start: 0.8822 (tttt) cc_final: 0.8133 (ttmm) REVERT: D 223 LEU cc_start: 0.9025 (mt) cc_final: 0.8235 (tp) REVERT: D 230 ILE cc_start: 0.9604 (mt) cc_final: 0.9399 (mp) REVERT: D 306 PHE cc_start: 0.7580 (t80) cc_final: 0.7085 (t80) REVERT: D 433 PHE cc_start: 0.8640 (t80) cc_final: 0.8415 (t80) REVERT: E 203 ILE cc_start: 0.8721 (pp) cc_final: 0.8493 (pp) REVERT: E 250 TYR cc_start: 0.7105 (p90) cc_final: 0.6874 (p90) REVERT: E 334 ASN cc_start: 0.8913 (m-40) cc_final: 0.8631 (m110) REVERT: L 3 GLN cc_start: 0.8303 (mp10) cc_final: 0.6900 (mp10) REVERT: L 468 LEU cc_start: 0.8918 (tp) cc_final: 0.8582 (tt) REVERT: L 472 ASN cc_start: 0.8462 (t0) cc_final: 0.7939 (t0) REVERT: M 468 LEU cc_start: 0.8661 (tp) cc_final: 0.8450 (tp) REVERT: M 472 ASN cc_start: 0.8723 (t0) cc_final: 0.7843 (t0) REVERT: M 482 TYR cc_start: 0.8582 (m-80) cc_final: 0.8359 (m-80) outliers start: 8 outliers final: 3 residues processed: 431 average time/residue: 0.7160 time to fit residues: 335.0605 Evaluate side-chains 254 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain L residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0050 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 149 ASN A 345 ASN B 243 ASN B 267 HIS D 90 GLN D 267 HIS E 77 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 233 GLN E 240 HIS ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062058 restraints weight = 64189.104| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.15 r_work: 0.2794 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16132 Z= 0.151 Angle : 0.661 13.807 21964 Z= 0.345 Chirality : 0.045 0.175 2510 Planarity : 0.004 0.064 2682 Dihedral : 9.022 77.766 2673 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.88 % Allowed : 14.05 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1863 helix: 1.71 (0.21), residues: 576 sheet: 0.37 (0.23), residues: 488 loop : 0.78 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 96 TYR 0.023 0.002 TYR B 299 PHE 0.028 0.002 PHE B 293 TRP 0.035 0.001 TRP E 315 HIS 0.008 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00331 (16099) covalent geometry : angle 0.65426 (21872) SS BOND : bond 0.00194 ( 7) SS BOND : angle 0.44796 ( 14) hydrogen bonds : bond 0.04768 ( 793) hydrogen bonds : angle 5.11098 ( 2537) link_ALPHA1-3 : bond 0.00769 ( 3) link_ALPHA1-3 : angle 2.21300 ( 9) link_ALPHA1-6 : bond 0.00615 ( 3) link_ALPHA1-6 : angle 1.62924 ( 9) link_BETA1-4 : bond 0.00283 ( 11) link_BETA1-4 : angle 1.75727 ( 33) link_NAG-ASN : bond 0.00239 ( 9) link_NAG-ASN : angle 1.40524 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8689 (mtm) cc_final: 0.8336 (mmm) REVERT: A 92 GLU cc_start: 0.8568 (pt0) cc_final: 0.7953 (pm20) REVERT: A 260 MET cc_start: 0.8629 (tpp) cc_final: 0.8420 (tpp) REVERT: A 262 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8956 (mm-40) REVERT: A 321 TRP cc_start: 0.7700 (m-10) cc_final: 0.6852 (m100) REVERT: A 335 ILE cc_start: 0.9481 (mm) cc_final: 0.9276 (mm) REVERT: B 13 LYS cc_start: 0.8721 (tttt) cc_final: 0.8390 (ttpp) REVERT: B 215 LYS cc_start: 0.9270 (tttt) cc_final: 0.8948 (ttmm) REVERT: B 269 ARG cc_start: 0.8670 (ptm160) cc_final: 0.8360 (ptm160) REVERT: B 298 GLU cc_start: 0.9222 (tm-30) cc_final: 0.9014 (tm-30) REVERT: B 306 PHE cc_start: 0.8105 (t80) cc_final: 0.7481 (t80) REVERT: C 9 MET cc_start: 0.8509 (mtp) cc_final: 0.8026 (mtt) REVERT: C 90 GLN cc_start: 0.9000 (mp10) cc_final: 0.8137 (mp10) REVERT: C 278 VAL cc_start: 0.8597 (t) cc_final: 0.8367 (p) REVERT: C 286 MET cc_start: 0.9103 (mmp) cc_final: 0.8606 (mmm) REVERT: C 302 VAL cc_start: 0.9355 (t) cc_final: 0.9084 (t) REVERT: C 440 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9038 (tp) REVERT: D 13 LYS cc_start: 0.9185 (tttt) cc_final: 0.8532 (tmmt) REVERT: D 21 LYS cc_start: 0.8357 (mmmm) cc_final: 0.7975 (mmmm) REVERT: D 147 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 215 LYS cc_start: 0.9092 (tttt) cc_final: 0.8610 (tttp) REVERT: D 243 ASN cc_start: 0.8390 (t0) cc_final: 0.8022 (t0) REVERT: D 306 PHE cc_start: 0.7904 (t80) cc_final: 0.7294 (t80) REVERT: D 433 PHE cc_start: 0.8944 (t80) cc_final: 0.8709 (t80) REVERT: E 118 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8076 (mppt) REVERT: E 142 LYS cc_start: 0.9254 (mtmt) cc_final: 0.9009 (mtmm) REVERT: E 233 GLN cc_start: 0.8215 (tt0) cc_final: 0.7873 (tp40) REVERT: E 435 PHE cc_start: 0.8670 (m-80) cc_final: 0.8197 (m-80) REVERT: L 3 GLN cc_start: 0.8177 (mp10) cc_final: 0.7413 (mp10) REVERT: L 472 ASN cc_start: 0.8854 (t0) cc_final: 0.7972 (t0) REVERT: L 474 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8156 (mptm) REVERT: M 11 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7363 (tm) REVERT: M 452 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8692 (ttmm) REVERT: M 472 ASN cc_start: 0.8765 (t0) cc_final: 0.8129 (t0) REVERT: M 473 LEU cc_start: 0.9382 (mt) cc_final: 0.9101 (mm) REVERT: M 474 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8318 (mmmt) outliers start: 48 outliers final: 9 residues processed: 309 average time/residue: 0.7119 time to fit residues: 239.4159 Evaluate side-chains 248 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 0.0470 chunk 73 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 267 HIS C 267 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 227 ASN E 253 GLN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 ASN L 504 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.084515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.062572 restraints weight = 53172.787| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.83 r_work: 0.2814 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16132 Z= 0.125 Angle : 0.609 10.208 21964 Z= 0.313 Chirality : 0.044 0.208 2510 Planarity : 0.004 0.035 2682 Dihedral : 7.369 70.591 2666 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.98 % Allowed : 15.01 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1863 helix: 1.77 (0.21), residues: 569 sheet: 0.56 (0.23), residues: 493 loop : 0.75 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 96 TYR 0.022 0.001 TYR B 299 PHE 0.021 0.002 PHE B 306 TRP 0.017 0.001 TRP L 440 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00276 (16099) covalent geometry : angle 0.60266 (21872) SS BOND : bond 0.00251 ( 7) SS BOND : angle 0.27470 ( 14) hydrogen bonds : bond 0.03973 ( 793) hydrogen bonds : angle 4.66450 ( 2537) link_ALPHA1-3 : bond 0.01006 ( 3) link_ALPHA1-3 : angle 1.70035 ( 9) link_ALPHA1-6 : bond 0.00724 ( 3) link_ALPHA1-6 : angle 1.79142 ( 9) link_BETA1-4 : bond 0.00376 ( 11) link_BETA1-4 : angle 1.64623 ( 33) link_NAG-ASN : bond 0.00245 ( 9) link_NAG-ASN : angle 1.34984 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8752 (mtm) cc_final: 0.8367 (mmm) REVERT: A 92 GLU cc_start: 0.8583 (pt0) cc_final: 0.7978 (pm20) REVERT: A 260 MET cc_start: 0.8618 (tpp) cc_final: 0.8384 (tpp) REVERT: A 262 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8596 (mm-40) REVERT: A 321 TRP cc_start: 0.7665 (m-10) cc_final: 0.6794 (m100) REVERT: A 345 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8193 (m-40) REVERT: B 13 LYS cc_start: 0.8807 (tttt) cc_final: 0.8468 (ttpp) REVERT: B 18 LYS cc_start: 0.9186 (pttp) cc_final: 0.8947 (pptt) REVERT: B 89 ASP cc_start: 0.8651 (m-30) cc_final: 0.8255 (m-30) REVERT: B 215 LYS cc_start: 0.9262 (tttt) cc_final: 0.8937 (ttmm) REVERT: B 269 ARG cc_start: 0.8766 (ptm160) cc_final: 0.7885 (ttm-80) REVERT: B 274 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8563 (tmtp) REVERT: B 306 PHE cc_start: 0.8016 (t80) cc_final: 0.7670 (t80) REVERT: C 9 MET cc_start: 0.8468 (mtp) cc_final: 0.8057 (mtt) REVERT: C 90 GLN cc_start: 0.8971 (mp10) cc_final: 0.8147 (mp10) REVERT: C 230 ILE cc_start: 0.9676 (mt) cc_final: 0.9330 (mp) REVERT: C 286 MET cc_start: 0.9048 (mmp) cc_final: 0.8600 (mmm) REVERT: D 13 LYS cc_start: 0.9193 (tttt) cc_final: 0.8558 (tmmt) REVERT: D 21 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8102 (mmmm) REVERT: D 147 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7712 (mm-30) REVERT: D 215 LYS cc_start: 0.9109 (tttt) cc_final: 0.8664 (tttp) REVERT: D 243 ASN cc_start: 0.8448 (t0) cc_final: 0.7966 (t0) REVERT: D 306 PHE cc_start: 0.7728 (t80) cc_final: 0.7485 (t80) REVERT: D 433 PHE cc_start: 0.8943 (t80) cc_final: 0.8685 (t80) REVERT: E 142 LYS cc_start: 0.9217 (mtmt) cc_final: 0.9011 (mtmm) REVERT: E 224 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: E 226 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7401 (ppp) REVERT: E 435 PHE cc_start: 0.8781 (m-80) cc_final: 0.8530 (m-80) REVERT: L 3 GLN cc_start: 0.8192 (mp10) cc_final: 0.7575 (mp10) REVERT: L 469 GLU cc_start: 0.8286 (mp0) cc_final: 0.8032 (mp0) REVERT: L 472 ASN cc_start: 0.8888 (t0) cc_final: 0.8400 (t0) REVERT: M 11 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7228 (tm) REVERT: M 469 GLU cc_start: 0.7590 (mp0) cc_final: 0.7196 (mp0) REVERT: M 472 ASN cc_start: 0.8899 (t0) cc_final: 0.8295 (t0) REVERT: M 473 LEU cc_start: 0.9426 (mt) cc_final: 0.8916 (mm) REVERT: M 474 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8375 (mmmt) REVERT: M 504 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8570 (pm20) outliers start: 33 outliers final: 7 residues processed: 279 average time/residue: 0.6897 time to fit residues: 209.7757 Evaluate side-chains 244 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 504 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 62 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 30 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN C 267 HIS C 303 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 227 ASN E 253 GLN L 1 GLN L 3 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.059480 restraints weight = 59111.653| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 4.00 r_work: 0.2735 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16132 Z= 0.213 Angle : 0.650 11.566 21964 Z= 0.332 Chirality : 0.045 0.217 2510 Planarity : 0.004 0.057 2682 Dihedral : 6.784 67.124 2666 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.40 % Allowed : 15.67 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1863 helix: 1.74 (0.21), residues: 569 sheet: 0.64 (0.23), residues: 493 loop : 0.68 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 50 TYR 0.028 0.002 TYR B 299 PHE 0.018 0.002 PHE C 293 TRP 0.021 0.002 TRP L 440 HIS 0.007 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00488 (16099) covalent geometry : angle 0.64289 (21872) SS BOND : bond 0.00211 ( 7) SS BOND : angle 0.58719 ( 14) hydrogen bonds : bond 0.03860 ( 793) hydrogen bonds : angle 4.59236 ( 2537) link_ALPHA1-3 : bond 0.00859 ( 3) link_ALPHA1-3 : angle 1.85883 ( 9) link_ALPHA1-6 : bond 0.00612 ( 3) link_ALPHA1-6 : angle 1.76316 ( 9) link_BETA1-4 : bond 0.00336 ( 11) link_BETA1-4 : angle 1.91058 ( 33) link_NAG-ASN : bond 0.00115 ( 9) link_NAG-ASN : angle 1.49682 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8743 (mtm) cc_final: 0.8451 (mmm) REVERT: A 92 GLU cc_start: 0.8622 (pt0) cc_final: 0.8006 (pm20) REVERT: A 260 MET cc_start: 0.8671 (tpp) cc_final: 0.8435 (tpp) REVERT: A 262 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8592 (mm-40) REVERT: A 321 TRP cc_start: 0.7701 (m-10) cc_final: 0.6811 (m100) REVERT: B 13 LYS cc_start: 0.8897 (tttt) cc_final: 0.8529 (ttpp) REVERT: B 18 LYS cc_start: 0.9243 (pttp) cc_final: 0.8996 (pptt) REVERT: B 215 LYS cc_start: 0.9296 (tttt) cc_final: 0.8979 (ttmm) REVERT: B 269 ARG cc_start: 0.8775 (ptm160) cc_final: 0.7946 (ttm-80) REVERT: B 274 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8584 (tmtp) REVERT: B 278 VAL cc_start: 0.8458 (t) cc_final: 0.8159 (p) REVERT: C 9 MET cc_start: 0.8481 (mtp) cc_final: 0.8056 (mtt) REVERT: C 90 GLN cc_start: 0.8987 (mp10) cc_final: 0.8125 (mp10) REVERT: C 424 ASP cc_start: 0.9173 (m-30) cc_final: 0.8884 (m-30) REVERT: D 13 LYS cc_start: 0.9204 (tttt) cc_final: 0.8559 (tmmt) REVERT: D 21 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8284 (mmmm) REVERT: D 112 LYS cc_start: 0.9073 (mmtp) cc_final: 0.8821 (mmtm) REVERT: D 147 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 215 LYS cc_start: 0.9184 (tttt) cc_final: 0.8717 (tttp) REVERT: D 243 ASN cc_start: 0.8430 (t0) cc_final: 0.7895 (t0) REVERT: D 306 PHE cc_start: 0.7793 (t80) cc_final: 0.7536 (t80) REVERT: D 433 PHE cc_start: 0.8981 (t80) cc_final: 0.8749 (t80) REVERT: E 118 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8206 (mppt) REVERT: E 179 MET cc_start: 0.8833 (mpp) cc_final: 0.8506 (tpp) REVERT: E 213 GLN cc_start: 0.8760 (tt0) cc_final: 0.8559 (tt0) REVERT: E 224 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: L 3 GLN cc_start: 0.8423 (mp-120) cc_final: 0.7574 (mp10) REVERT: L 469 GLU cc_start: 0.8196 (mp0) cc_final: 0.7967 (mp0) REVERT: L 472 ASN cc_start: 0.8986 (t0) cc_final: 0.8445 (t0) REVERT: M 11 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7264 (tm) REVERT: M 469 GLU cc_start: 0.7879 (mp0) cc_final: 0.7459 (mp0) REVERT: M 472 ASN cc_start: 0.9018 (t0) cc_final: 0.8539 (t0) REVERT: M 473 LEU cc_start: 0.9417 (mt) cc_final: 0.8761 (mm) REVERT: M 474 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8343 (mmmt) outliers start: 40 outliers final: 9 residues processed: 265 average time/residue: 0.7002 time to fit residues: 201.7796 Evaluate side-chains 252 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 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 = 0.3422 r_free = 0.3422 target = 0.083027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.061586 restraints weight = 41992.170| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.41 r_work: 0.2799 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16132 Z= 0.135 Angle : 0.604 9.729 21964 Z= 0.308 Chirality : 0.044 0.224 2510 Planarity : 0.003 0.027 2682 Dihedral : 6.254 61.334 2666 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.92 % Allowed : 16.63 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1863 helix: 1.81 (0.21), residues: 570 sheet: 0.67 (0.23), residues: 503 loop : 0.68 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.026 0.001 TYR B 299 PHE 0.019 0.001 PHE C 293 TRP 0.022 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00303 (16099) covalent geometry : angle 0.59833 (21872) SS BOND : bond 0.00140 ( 7) SS BOND : angle 0.41278 ( 14) hydrogen bonds : bond 0.03559 ( 793) hydrogen bonds : angle 4.44219 ( 2537) link_ALPHA1-3 : bond 0.00952 ( 3) link_ALPHA1-3 : angle 1.70058 ( 9) link_ALPHA1-6 : bond 0.00772 ( 3) link_ALPHA1-6 : angle 1.67502 ( 9) link_BETA1-4 : bond 0.00317 ( 11) link_BETA1-4 : angle 1.60500 ( 33) link_NAG-ASN : bond 0.00088 ( 9) link_NAG-ASN : angle 1.38680 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8712 (mtm) cc_final: 0.8339 (mmm) REVERT: A 92 GLU cc_start: 0.8564 (pt0) cc_final: 0.7938 (pm20) REVERT: A 260 MET cc_start: 0.8559 (tpp) cc_final: 0.8307 (tpp) REVERT: A 321 TRP cc_start: 0.7624 (m-10) cc_final: 0.6741 (m100) REVERT: B 13 LYS cc_start: 0.8840 (tttt) cc_final: 0.8517 (ttpp) REVERT: B 18 LYS cc_start: 0.9228 (pttp) cc_final: 0.8928 (pptt) REVERT: B 147 GLU cc_start: 0.8698 (tt0) cc_final: 0.8446 (tt0) REVERT: B 190 GLU cc_start: 0.8836 (tt0) cc_final: 0.8203 (pt0) REVERT: B 215 LYS cc_start: 0.9249 (tttt) cc_final: 0.8919 (ttmm) REVERT: B 274 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8556 (tmtp) REVERT: B 278 VAL cc_start: 0.8442 (t) cc_final: 0.8209 (p) REVERT: B 306 PHE cc_start: 0.7791 (t80) cc_final: 0.7590 (t80) REVERT: C 9 MET cc_start: 0.8504 (mtp) cc_final: 0.8139 (ttm) REVERT: C 90 GLN cc_start: 0.8954 (mp10) cc_final: 0.8078 (mp10) REVERT: C 244 TYR cc_start: 0.8818 (p90) cc_final: 0.8607 (p90) REVERT: C 424 ASP cc_start: 0.9101 (m-30) cc_final: 0.8761 (m-30) REVERT: D 13 LYS cc_start: 0.9235 (tttt) cc_final: 0.8478 (tmmt) REVERT: D 21 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8378 (mmmm) REVERT: D 112 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8826 (mmtm) REVERT: D 147 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7548 (mm-30) REVERT: D 215 LYS cc_start: 0.9169 (tttt) cc_final: 0.8692 (ttmm) REVERT: D 227 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8651 (tpt) REVERT: D 243 ASN cc_start: 0.8411 (t0) cc_final: 0.7911 (t0) REVERT: D 306 PHE cc_start: 0.7731 (t80) cc_final: 0.7511 (t80) REVERT: D 426 TRP cc_start: 0.8671 (m100) cc_final: 0.8414 (t-100) REVERT: D 433 PHE cc_start: 0.8959 (t80) cc_final: 0.8696 (t80) REVERT: E 116 VAL cc_start: 0.9247 (t) cc_final: 0.9031 (m) REVERT: E 118 LYS cc_start: 0.9032 (mmtm) cc_final: 0.8471 (mmtm) REVERT: E 179 MET cc_start: 0.8648 (mpp) cc_final: 0.8345 (tpp) REVERT: E 213 GLN cc_start: 0.8777 (tt0) cc_final: 0.8453 (tt0) REVERT: E 224 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: E 226 MET cc_start: 0.8011 (ppp) cc_final: 0.7777 (ppp) REVERT: E 313 TYR cc_start: 0.9373 (t80) cc_final: 0.9112 (t80) REVERT: L 3 GLN cc_start: 0.8363 (mp-120) cc_final: 0.7736 (mp10) REVERT: L 469 GLU cc_start: 0.8181 (mp0) cc_final: 0.7902 (mp0) REVERT: L 472 ASN cc_start: 0.8998 (t0) cc_final: 0.8536 (t0) REVERT: M 11 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7318 (tm) REVERT: M 464 ASN cc_start: 0.8987 (m-40) cc_final: 0.8691 (p0) REVERT: M 467 TYR cc_start: 0.8367 (m-80) cc_final: 0.8050 (m-80) REVERT: M 469 GLU cc_start: 0.7983 (mp0) cc_final: 0.7440 (mp0) REVERT: M 472 ASN cc_start: 0.9047 (t0) cc_final: 0.8412 (t0) REVERT: M 473 LEU cc_start: 0.9336 (mt) cc_final: 0.9023 (mm) REVERT: M 474 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8218 (mmpt) outliers start: 32 outliers final: 13 residues processed: 284 average time/residue: 0.7269 time to fit residues: 224.9587 Evaluate side-chains 258 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 132 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN D 224 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058237 restraints weight = 66658.998| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 4.15 r_work: 0.2707 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16132 Z= 0.224 Angle : 0.662 9.541 21964 Z= 0.339 Chirality : 0.045 0.231 2510 Planarity : 0.004 0.050 2682 Dihedral : 6.215 59.469 2666 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.58 % Allowed : 16.27 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1863 helix: 1.71 (0.21), residues: 569 sheet: 0.67 (0.23), residues: 502 loop : 0.63 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 114 TYR 0.033 0.002 TYR D 220 PHE 0.017 0.002 PHE C 293 TRP 0.029 0.002 TRP L 440 HIS 0.005 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00509 (16099) covalent geometry : angle 0.65551 (21872) SS BOND : bond 0.00181 ( 7) SS BOND : angle 0.62114 ( 14) hydrogen bonds : bond 0.03788 ( 793) hydrogen bonds : angle 4.51766 ( 2537) link_ALPHA1-3 : bond 0.00814 ( 3) link_ALPHA1-3 : angle 1.86313 ( 9) link_ALPHA1-6 : bond 0.00653 ( 3) link_ALPHA1-6 : angle 1.73232 ( 9) link_BETA1-4 : bond 0.00333 ( 11) link_BETA1-4 : angle 1.84937 ( 33) link_NAG-ASN : bond 0.00133 ( 9) link_NAG-ASN : angle 1.55056 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8770 (mtm) cc_final: 0.8389 (mmm) REVERT: A 92 GLU cc_start: 0.8681 (pt0) cc_final: 0.8035 (pm20) REVERT: A 181 MET cc_start: 0.8737 (mtm) cc_final: 0.8499 (pmm) REVERT: A 321 TRP cc_start: 0.7759 (m-10) cc_final: 0.6877 (m100) REVERT: B 13 LYS cc_start: 0.8895 (tttt) cc_final: 0.8528 (ttpp) REVERT: B 18 LYS cc_start: 0.9199 (pttp) cc_final: 0.8928 (pptt) REVERT: B 147 GLU cc_start: 0.8809 (tt0) cc_final: 0.8543 (tt0) REVERT: B 190 GLU cc_start: 0.8894 (tt0) cc_final: 0.8593 (pt0) REVERT: B 215 LYS cc_start: 0.9355 (tttt) cc_final: 0.9033 (ttmm) REVERT: B 269 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8492 (ttm-80) REVERT: B 274 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8572 (tmtp) REVERT: B 278 VAL cc_start: 0.8595 (t) cc_final: 0.8391 (p) REVERT: C 9 MET cc_start: 0.8466 (mtp) cc_final: 0.8100 (ttm) REVERT: C 90 GLN cc_start: 0.8940 (mp10) cc_final: 0.8025 (mp10) REVERT: C 244 TYR cc_start: 0.8892 (p90) cc_final: 0.8606 (p90) REVERT: C 424 ASP cc_start: 0.9136 (m-30) cc_final: 0.8807 (m-30) REVERT: D 13 LYS cc_start: 0.9146 (tttt) cc_final: 0.8505 (tmmt) REVERT: D 21 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8405 (mmmm) REVERT: D 112 LYS cc_start: 0.9123 (mmtp) cc_final: 0.8882 (mmtm) REVERT: D 147 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7708 (mm-30) REVERT: D 215 LYS cc_start: 0.9242 (tttt) cc_final: 0.8679 (ttmm) REVERT: D 227 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8681 (tpt) REVERT: D 243 ASN cc_start: 0.8423 (t0) cc_final: 0.7840 (t0) REVERT: D 306 PHE cc_start: 0.7775 (t80) cc_final: 0.7561 (t80) REVERT: D 426 TRP cc_start: 0.8726 (m100) cc_final: 0.8482 (t-100) REVERT: D 433 PHE cc_start: 0.9010 (t80) cc_final: 0.8751 (t80) REVERT: E 116 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9033 (m) REVERT: E 118 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8274 (mppt) REVERT: E 179 MET cc_start: 0.8769 (mpp) cc_final: 0.8497 (tpp) REVERT: E 213 GLN cc_start: 0.8904 (tt0) cc_final: 0.8619 (tt0) REVERT: E 224 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: E 226 MET cc_start: 0.8062 (ppp) cc_final: 0.7770 (ppp) REVERT: E 228 PHE cc_start: 0.8536 (m-80) cc_final: 0.8282 (m-80) REVERT: L 1 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6621 (pp30) REVERT: L 3 GLN cc_start: 0.8520 (mp-120) cc_final: 0.7966 (mp10) REVERT: L 430 LYS cc_start: 0.8930 (mppt) cc_final: 0.8454 (mptt) REVERT: L 469 GLU cc_start: 0.8211 (mp0) cc_final: 0.7965 (mp0) REVERT: L 472 ASN cc_start: 0.9088 (t0) cc_final: 0.8625 (t0) REVERT: L 476 GLU cc_start: 0.8527 (mp0) cc_final: 0.8241 (pm20) REVERT: M 11 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7486 (tm) REVERT: M 452 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8613 (ttmm) REVERT: M 459 ARG cc_start: 0.8015 (ppt90) cc_final: 0.7664 (ptt-90) REVERT: M 460 ASP cc_start: 0.7737 (p0) cc_final: 0.6455 (p0) REVERT: M 464 ASN cc_start: 0.9005 (m110) cc_final: 0.8755 (p0) REVERT: M 467 TYR cc_start: 0.8481 (m-80) cc_final: 0.8014 (m-80) REVERT: M 469 GLU cc_start: 0.8193 (mp0) cc_final: 0.7571 (mp0) REVERT: M 472 ASN cc_start: 0.9101 (t0) cc_final: 0.8418 (t0) REVERT: M 473 LEU cc_start: 0.9295 (mt) cc_final: 0.9018 (mm) REVERT: M 474 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8285 (mmpt) outliers start: 43 outliers final: 18 residues processed: 275 average time/residue: 0.7408 time to fit residues: 221.8406 Evaluate side-chains 258 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN C 224 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060575 restraints weight = 66429.976| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.14 r_work: 0.2747 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16132 Z= 0.129 Angle : 0.629 9.794 21964 Z= 0.319 Chirality : 0.044 0.226 2510 Planarity : 0.004 0.055 2682 Dihedral : 5.860 54.704 2666 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.16 % Allowed : 17.71 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1863 helix: 1.75 (0.21), residues: 571 sheet: 0.71 (0.23), residues: 501 loop : 0.64 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 307 TYR 0.025 0.001 TYR D 220 PHE 0.014 0.001 PHE B 293 TRP 0.025 0.001 TRP L 440 HIS 0.002 0.000 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00289 (16099) covalent geometry : angle 0.62371 (21872) SS BOND : bond 0.00079 ( 7) SS BOND : angle 0.42594 ( 14) hydrogen bonds : bond 0.03511 ( 793) hydrogen bonds : angle 4.40792 ( 2537) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 1.66142 ( 9) link_ALPHA1-6 : bond 0.00839 ( 3) link_ALPHA1-6 : angle 1.57713 ( 9) link_BETA1-4 : bond 0.00320 ( 11) link_BETA1-4 : angle 1.51025 ( 33) link_NAG-ASN : bond 0.00116 ( 9) link_NAG-ASN : angle 1.39673 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8809 (mtm) cc_final: 0.8426 (mmm) REVERT: A 92 GLU cc_start: 0.8642 (pt0) cc_final: 0.8010 (pm20) REVERT: A 181 MET cc_start: 0.8772 (mtm) cc_final: 0.8499 (pmm) REVERT: A 262 GLN cc_start: 0.9056 (mt0) cc_final: 0.8807 (mt0) REVERT: A 267 CYS cc_start: 0.9253 (m) cc_final: 0.8993 (m) REVERT: A 282 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8607 (ptpp) REVERT: A 321 TRP cc_start: 0.7752 (m-10) cc_final: 0.6858 (m100) REVERT: B 147 GLU cc_start: 0.8742 (tt0) cc_final: 0.8462 (tt0) REVERT: B 190 GLU cc_start: 0.8902 (tt0) cc_final: 0.8647 (pt0) REVERT: B 274 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8691 (ttmm) REVERT: B 298 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8982 (tm-30) REVERT: C 9 MET cc_start: 0.8497 (mtp) cc_final: 0.8127 (ttm) REVERT: C 90 GLN cc_start: 0.8911 (mp10) cc_final: 0.8006 (mp10) REVERT: C 244 TYR cc_start: 0.8871 (p90) cc_final: 0.8601 (p90) REVERT: C 424 ASP cc_start: 0.9063 (m-30) cc_final: 0.8758 (m-30) REVERT: D 13 LYS cc_start: 0.9128 (tttt) cc_final: 0.8504 (tmmt) REVERT: D 21 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8403 (mmmm) REVERT: D 112 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8898 (mmtm) REVERT: D 147 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7721 (mm-30) REVERT: D 215 LYS cc_start: 0.9233 (tttt) cc_final: 0.8695 (ttmm) REVERT: D 224 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8838 (pt0) REVERT: D 243 ASN cc_start: 0.8428 (t0) cc_final: 0.7889 (t0) REVERT: D 426 TRP cc_start: 0.8689 (m100) cc_final: 0.8458 (t-100) REVERT: D 433 PHE cc_start: 0.8987 (t80) cc_final: 0.8739 (t80) REVERT: E 82 ASN cc_start: 0.9124 (m-40) cc_final: 0.8808 (m-40) REVERT: E 116 VAL cc_start: 0.9284 (t) cc_final: 0.9052 (m) REVERT: E 118 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8268 (mppt) REVERT: E 179 MET cc_start: 0.8758 (mpp) cc_final: 0.8504 (tpp) REVERT: E 213 GLN cc_start: 0.8847 (tt0) cc_final: 0.8526 (tt0) REVERT: E 224 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: E 226 MET cc_start: 0.8036 (ppp) cc_final: 0.7817 (ppp) REVERT: E 253 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8072 (pp30) REVERT: E 313 TYR cc_start: 0.9426 (t80) cc_final: 0.9051 (t80) REVERT: L 1 GLN cc_start: 0.6801 (tm-30) cc_final: 0.6575 (pp30) REVERT: L 3 GLN cc_start: 0.8571 (mp-120) cc_final: 0.8106 (mp10) REVERT: L 469 GLU cc_start: 0.8209 (mp0) cc_final: 0.7910 (mp0) REVERT: L 472 ASN cc_start: 0.9141 (t0) cc_final: 0.8708 (t0) REVERT: L 476 GLU cc_start: 0.8540 (mp0) cc_final: 0.8280 (pm20) REVERT: M 11 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7529 (tm) REVERT: M 460 ASP cc_start: 0.7498 (p0) cc_final: 0.7182 (p0) REVERT: M 469 GLU cc_start: 0.8212 (mp0) cc_final: 0.7585 (mp0) REVERT: M 472 ASN cc_start: 0.9091 (t0) cc_final: 0.8444 (t0) REVERT: M 473 LEU cc_start: 0.9255 (mt) cc_final: 0.8979 (mm) REVERT: M 474 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8321 (mmpt) outliers start: 36 outliers final: 12 residues processed: 271 average time/residue: 0.6601 time to fit residues: 195.5577 Evaluate side-chains 253 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 184 optimal weight: 0.0040 chunk 162 optimal weight: 6.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060911 restraints weight = 58851.776| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.92 r_work: 0.2765 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16132 Z= 0.142 Angle : 0.636 9.847 21964 Z= 0.323 Chirality : 0.044 0.229 2510 Planarity : 0.003 0.027 2682 Dihedral : 5.703 52.433 2666 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.80 % Allowed : 18.01 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1863 helix: 1.68 (0.21), residues: 570 sheet: 0.72 (0.23), residues: 501 loop : 0.62 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 459 TYR 0.026 0.001 TYR B 299 PHE 0.026 0.001 PHE C 293 TRP 0.019 0.001 TRP L 440 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00323 (16099) covalent geometry : angle 0.63074 (21872) SS BOND : bond 0.00097 ( 7) SS BOND : angle 0.48295 ( 14) hydrogen bonds : bond 0.03494 ( 793) hydrogen bonds : angle 4.38812 ( 2537) link_ALPHA1-3 : bond 0.00877 ( 3) link_ALPHA1-3 : angle 1.72015 ( 9) link_ALPHA1-6 : bond 0.00806 ( 3) link_ALPHA1-6 : angle 1.56135 ( 9) link_BETA1-4 : bond 0.00314 ( 11) link_BETA1-4 : angle 1.52620 ( 33) link_NAG-ASN : bond 0.00087 ( 9) link_NAG-ASN : angle 1.37657 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8814 (mtm) cc_final: 0.8400 (mmm) REVERT: A 92 GLU cc_start: 0.8617 (pt0) cc_final: 0.8019 (pm20) REVERT: A 160 ILE cc_start: 0.9386 (mt) cc_final: 0.9167 (mp) REVERT: A 181 MET cc_start: 0.8760 (mtm) cc_final: 0.8491 (pmm) REVERT: A 267 CYS cc_start: 0.9207 (m) cc_final: 0.8931 (m) REVERT: A 321 TRP cc_start: 0.7712 (m-10) cc_final: 0.6852 (m100) REVERT: B 49 MET cc_start: 0.8787 (ttp) cc_final: 0.8120 (tmm) REVERT: B 147 GLU cc_start: 0.8719 (tt0) cc_final: 0.8453 (tt0) REVERT: B 190 GLU cc_start: 0.8860 (tt0) cc_final: 0.8604 (pt0) REVERT: B 269 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8205 (ttm-80) REVERT: B 274 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8702 (ttmm) REVERT: B 298 GLU cc_start: 0.9275 (tm-30) cc_final: 0.9044 (tm-30) REVERT: C 9 MET cc_start: 0.8496 (mtp) cc_final: 0.8114 (ttm) REVERT: C 90 GLN cc_start: 0.8904 (mp10) cc_final: 0.7980 (mp10) REVERT: C 244 TYR cc_start: 0.8857 (p90) cc_final: 0.8581 (p90) REVERT: C 424 ASP cc_start: 0.9022 (m-30) cc_final: 0.8707 (m-30) REVERT: D 13 LYS cc_start: 0.9153 (tttt) cc_final: 0.8518 (tmmt) REVERT: D 21 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8404 (mmmm) REVERT: D 112 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8860 (mmtm) REVERT: D 147 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 190 GLU cc_start: 0.8625 (tt0) cc_final: 0.8302 (tt0) REVERT: D 215 LYS cc_start: 0.9223 (tttt) cc_final: 0.8696 (ttmm) REVERT: D 224 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8843 (pm20) REVERT: D 243 ASN cc_start: 0.8409 (t0) cc_final: 0.7838 (t0) REVERT: D 426 TRP cc_start: 0.8650 (m100) cc_final: 0.8429 (t-100) REVERT: D 433 PHE cc_start: 0.8971 (t80) cc_final: 0.8723 (t80) REVERT: E 82 ASN cc_start: 0.9102 (m-40) cc_final: 0.8775 (m-40) REVERT: E 116 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9074 (m) REVERT: E 118 LYS cc_start: 0.9101 (mmtm) cc_final: 0.8525 (mmtm) REVERT: E 179 MET cc_start: 0.8693 (mpp) cc_final: 0.8448 (tpp) REVERT: E 213 GLN cc_start: 0.8850 (tt0) cc_final: 0.8543 (tt0) REVERT: E 224 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: E 226 MET cc_start: 0.7996 (ppp) cc_final: 0.7699 (ppp) REVERT: E 228 PHE cc_start: 0.8542 (m-80) cc_final: 0.8275 (m-10) REVERT: E 253 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8118 (pp30) REVERT: E 313 TYR cc_start: 0.9425 (t80) cc_final: 0.9065 (t80) REVERT: L 469 GLU cc_start: 0.8161 (mp0) cc_final: 0.7901 (mp0) REVERT: L 472 ASN cc_start: 0.9133 (t0) cc_final: 0.8681 (t0) REVERT: L 476 GLU cc_start: 0.8547 (mp0) cc_final: 0.8344 (pm20) REVERT: L 501 TYR cc_start: 0.9012 (m-80) cc_final: 0.8809 (m-10) REVERT: M 11 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7586 (tm) REVERT: M 455 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7060 (m-10) REVERT: M 460 ASP cc_start: 0.7247 (p0) cc_final: 0.6199 (p0) REVERT: M 467 TYR cc_start: 0.8438 (m-80) cc_final: 0.7895 (m-80) REVERT: M 469 GLU cc_start: 0.8269 (mp0) cc_final: 0.7640 (mp0) REVERT: M 472 ASN cc_start: 0.9086 (t0) cc_final: 0.8669 (t0) outliers start: 30 outliers final: 15 residues processed: 266 average time/residue: 0.6705 time to fit residues: 194.5390 Evaluate side-chains 256 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 455 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN L 3 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060830 restraints weight = 46047.179| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.52 r_work: 0.2783 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16132 Z= 0.156 Angle : 0.663 10.555 21964 Z= 0.335 Chirality : 0.045 0.228 2510 Planarity : 0.004 0.068 2682 Dihedral : 5.650 50.931 2666 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.92 % Allowed : 18.01 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1863 helix: 1.65 (0.21), residues: 570 sheet: 0.68 (0.23), residues: 501 loop : 0.59 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 114 TYR 0.026 0.002 TYR B 299 PHE 0.026 0.002 PHE B 306 TRP 0.019 0.001 TRP L 440 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00356 (16099) covalent geometry : angle 0.65819 (21872) SS BOND : bond 0.00094 ( 7) SS BOND : angle 0.60804 ( 14) hydrogen bonds : bond 0.03515 ( 793) hydrogen bonds : angle 4.44305 ( 2537) link_ALPHA1-3 : bond 0.00855 ( 3) link_ALPHA1-3 : angle 1.71904 ( 9) link_ALPHA1-6 : bond 0.00797 ( 3) link_ALPHA1-6 : angle 1.57534 ( 9) link_BETA1-4 : bond 0.00315 ( 11) link_BETA1-4 : angle 1.53877 ( 33) link_NAG-ASN : bond 0.00087 ( 9) link_NAG-ASN : angle 1.38501 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8733 (mtm) cc_final: 0.8396 (mmm) REVERT: A 92 GLU cc_start: 0.8581 (pt0) cc_final: 0.8018 (pm20) REVERT: A 160 ILE cc_start: 0.9380 (mt) cc_final: 0.9162 (mp) REVERT: A 181 MET cc_start: 0.8772 (mtm) cc_final: 0.8488 (pmm) REVERT: A 262 GLN cc_start: 0.9035 (mt0) cc_final: 0.8244 (mt0) REVERT: A 267 CYS cc_start: 0.9194 (m) cc_final: 0.8914 (m) REVERT: A 321 TRP cc_start: 0.7661 (m-10) cc_final: 0.6775 (m100) REVERT: B 49 MET cc_start: 0.8737 (ttp) cc_final: 0.7978 (pp-130) REVERT: B 147 GLU cc_start: 0.8669 (tt0) cc_final: 0.8403 (tt0) REVERT: B 190 GLU cc_start: 0.8820 (tt0) cc_final: 0.8564 (pt0) REVERT: B 269 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8336 (ttt90) REVERT: B 274 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8689 (ttmm) REVERT: C 9 MET cc_start: 0.8456 (mtp) cc_final: 0.8088 (ttm) REVERT: C 84 ASP cc_start: 0.8449 (t70) cc_final: 0.7965 (t70) REVERT: C 90 GLN cc_start: 0.8900 (mp10) cc_final: 0.7978 (mp10) REVERT: C 244 TYR cc_start: 0.8846 (p90) cc_final: 0.8582 (p90) REVERT: C 424 ASP cc_start: 0.8985 (m-30) cc_final: 0.8678 (m-30) REVERT: D 13 LYS cc_start: 0.9168 (tttt) cc_final: 0.8529 (tmmt) REVERT: D 112 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8846 (mmtm) REVERT: D 147 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 190 GLU cc_start: 0.8599 (tt0) cc_final: 0.8272 (tt0) REVERT: D 215 LYS cc_start: 0.9194 (tttt) cc_final: 0.8667 (ttmm) REVERT: D 243 ASN cc_start: 0.8442 (t0) cc_final: 0.7915 (t0) REVERT: D 426 TRP cc_start: 0.8634 (m100) cc_final: 0.8414 (t-100) REVERT: D 433 PHE cc_start: 0.8959 (t80) cc_final: 0.8720 (t80) REVERT: E 82 ASN cc_start: 0.9084 (m-40) cc_final: 0.8754 (m-40) REVERT: E 116 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9064 (m) REVERT: E 118 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8300 (mppt) REVERT: E 179 MET cc_start: 0.8689 (mpp) cc_final: 0.8458 (tpp) REVERT: E 213 GLN cc_start: 0.8843 (tt0) cc_final: 0.8537 (tt0) REVERT: E 224 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: E 226 MET cc_start: 0.8000 (ppp) cc_final: 0.7751 (ppp) REVERT: E 313 TYR cc_start: 0.9415 (t80) cc_final: 0.9042 (t80) REVERT: L 469 GLU cc_start: 0.8141 (mp0) cc_final: 0.7849 (mp0) REVERT: L 472 ASN cc_start: 0.9186 (t0) cc_final: 0.8772 (t0) REVERT: M 11 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7572 (tm) REVERT: M 455 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: M 460 ASP cc_start: 0.7017 (p0) cc_final: 0.6007 (p0) REVERT: M 467 TYR cc_start: 0.8325 (m-80) cc_final: 0.7158 (m-80) REVERT: M 469 GLU cc_start: 0.8302 (mp0) cc_final: 0.7632 (mp0) REVERT: M 472 ASN cc_start: 0.9070 (t0) cc_final: 0.8548 (t0) outliers start: 32 outliers final: 16 residues processed: 262 average time/residue: 0.6790 time to fit residues: 194.0783 Evaluate side-chains 257 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 106 optimal weight: 10.0000 chunk 158 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN D 224 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN M 3 GLN M 472 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.083476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060860 restraints weight = 58504.501| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.97 r_work: 0.2783 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16132 Z= 0.134 Angle : 0.672 11.352 21964 Z= 0.338 Chirality : 0.044 0.231 2510 Planarity : 0.003 0.028 2682 Dihedral : 5.469 48.123 2666 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 19.03 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1863 helix: 1.67 (0.21), residues: 569 sheet: 0.71 (0.23), residues: 501 loop : 0.58 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 459 TYR 0.028 0.001 TYR D 220 PHE 0.025 0.001 PHE C 293 TRP 0.021 0.001 TRP L 440 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00308 (16099) covalent geometry : angle 0.66767 (21872) SS BOND : bond 0.00063 ( 7) SS BOND : angle 0.48337 ( 14) hydrogen bonds : bond 0.03431 ( 793) hydrogen bonds : angle 4.42303 ( 2537) link_ALPHA1-3 : bond 0.00879 ( 3) link_ALPHA1-3 : angle 1.65833 ( 9) link_ALPHA1-6 : bond 0.00876 ( 3) link_ALPHA1-6 : angle 1.49869 ( 9) link_BETA1-4 : bond 0.00339 ( 11) link_BETA1-4 : angle 1.43675 ( 33) link_NAG-ASN : bond 0.00120 ( 9) link_NAG-ASN : angle 1.32714 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8837 (mtm) cc_final: 0.8424 (mmm) REVERT: A 92 GLU cc_start: 0.8639 (pt0) cc_final: 0.8086 (pm20) REVERT: A 160 ILE cc_start: 0.9378 (mt) cc_final: 0.9168 (mp) REVERT: A 181 MET cc_start: 0.8795 (mtm) cc_final: 0.8506 (pmm) REVERT: A 262 GLN cc_start: 0.9089 (mt0) cc_final: 0.8327 (mt0) REVERT: A 267 CYS cc_start: 0.9186 (m) cc_final: 0.8927 (m) REVERT: A 321 TRP cc_start: 0.7701 (m-10) cc_final: 0.6829 (m100) REVERT: B 49 MET cc_start: 0.8748 (ttp) cc_final: 0.7974 (pp-130) REVERT: B 147 GLU cc_start: 0.8692 (tt0) cc_final: 0.8434 (tt0) REVERT: B 190 GLU cc_start: 0.8831 (tt0) cc_final: 0.8530 (pt0) REVERT: B 274 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8668 (ttmm) REVERT: C 9 MET cc_start: 0.8446 (mtp) cc_final: 0.8063 (ttm) REVERT: C 84 ASP cc_start: 0.8436 (t70) cc_final: 0.7941 (t70) REVERT: C 90 GLN cc_start: 0.8890 (mp10) cc_final: 0.7961 (mp10) REVERT: C 190 GLU cc_start: 0.9027 (tt0) cc_final: 0.8680 (tt0) REVERT: C 244 TYR cc_start: 0.8877 (p90) cc_final: 0.8607 (p90) REVERT: C 424 ASP cc_start: 0.8950 (m-30) cc_final: 0.8603 (m-30) REVERT: D 13 LYS cc_start: 0.9134 (tttt) cc_final: 0.8507 (tmmt) REVERT: D 21 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8314 (mtmm) REVERT: D 112 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8844 (mmtm) REVERT: D 147 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7692 (mm-30) REVERT: D 190 GLU cc_start: 0.8634 (tt0) cc_final: 0.8278 (tt0) REVERT: D 215 LYS cc_start: 0.9208 (tttt) cc_final: 0.8693 (tttp) REVERT: D 243 ASN cc_start: 0.8469 (t0) cc_final: 0.7952 (t0) REVERT: D 426 TRP cc_start: 0.8672 (m100) cc_final: 0.8460 (t-100) REVERT: D 433 PHE cc_start: 0.8972 (t80) cc_final: 0.8738 (t80) REVERT: E 82 ASN cc_start: 0.9062 (m-40) cc_final: 0.8729 (m-40) REVERT: E 116 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9054 (m) REVERT: E 118 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8257 (mppt) REVERT: E 179 MET cc_start: 0.8711 (mpp) cc_final: 0.8469 (tpp) REVERT: E 213 GLN cc_start: 0.8856 (tt0) cc_final: 0.8561 (tt0) REVERT: E 224 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: E 226 MET cc_start: 0.8120 (ppp) cc_final: 0.7782 (ppp) REVERT: E 228 PHE cc_start: 0.8521 (m-80) cc_final: 0.8259 (m-10) REVERT: E 253 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8054 (pp30) REVERT: E 313 TYR cc_start: 0.9410 (t80) cc_final: 0.9022 (t80) REVERT: L 433 GLU cc_start: 0.8736 (pt0) cc_final: 0.8347 (pm20) REVERT: L 469 GLU cc_start: 0.8117 (mp0) cc_final: 0.7778 (mp0) REVERT: L 472 ASN cc_start: 0.9278 (t0) cc_final: 0.8897 (t0) REVERT: M 11 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7588 (tm) REVERT: M 455 PHE cc_start: 0.7659 (m-80) cc_final: 0.6950 (m-10) REVERT: M 469 GLU cc_start: 0.8343 (mp0) cc_final: 0.7724 (mp0) REVERT: M 472 ASN cc_start: 0.9073 (t0) cc_final: 0.8592 (t0) outliers start: 22 outliers final: 11 residues processed: 263 average time/residue: 0.6812 time to fit residues: 195.7304 Evaluate side-chains 256 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 33 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 22 optimal weight: 0.0270 chunk 174 optimal weight: 0.5980 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060523 restraints weight = 42229.218| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.38 r_work: 0.2785 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16132 Z= 0.180 Angle : 0.688 12.039 21964 Z= 0.347 Chirality : 0.045 0.228 2510 Planarity : 0.004 0.059 2682 Dihedral : 5.507 47.379 2666 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.56 % Allowed : 18.85 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1863 helix: 1.64 (0.21), residues: 570 sheet: 0.62 (0.23), residues: 504 loop : 0.55 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 307 TYR 0.028 0.002 TYR D 220 PHE 0.024 0.002 PHE C 293 TRP 0.017 0.001 TRP L 440 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00413 (16099) covalent geometry : angle 0.68276 (21872) SS BOND : bond 0.00127 ( 7) SS BOND : angle 0.50808 ( 14) hydrogen bonds : bond 0.03541 ( 793) hydrogen bonds : angle 4.48140 ( 2537) link_ALPHA1-3 : bond 0.00815 ( 3) link_ALPHA1-3 : angle 1.75482 ( 9) link_ALPHA1-6 : bond 0.00752 ( 3) link_ALPHA1-6 : angle 1.54137 ( 9) link_BETA1-4 : bond 0.00315 ( 11) link_BETA1-4 : angle 1.56882 ( 33) link_NAG-ASN : bond 0.00082 ( 9) link_NAG-ASN : angle 1.46284 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6416.71 seconds wall clock time: 109 minutes 54.03 seconds (6594.03 seconds total)