Starting phenix.real_space_refine on Fri Jul 3 20:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qn9_14071/07_2026/7qn9_14071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn9_14071/07_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_14071/07_2026/7qn9_14071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn9_14071/07_2026/7qn9_14071.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qn9_14071/07_2026/7qn9_14071.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qn9_14071/07_2026/7qn9_14071.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qn9_14071/07_2026/7qn9_14071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn9_14071/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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: 2.92, per 1000 atoms: 0.19 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: 1.06 Conformation dependent library (CDL) restraints added in 622.9 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: 0.52 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: 2.37 Time building geometry restraints manager: 1.38 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 - 17.66: 8675 17.66 - 35.33: 455 35.33 - 52.99: 70 52.99 - 70.65: 14 70.65 - 88.31: 13 Dihedral angle restraints: 9227 sinusoidal: 3662 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 9224 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: 2.110 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.030 Find NCS groups from input model: 0.290 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 11.486 88.315 5642 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/Z covalent geometry : bond 0.00309 / 0.14 (16099) covalent geometry : angle 0.63578 / 0.34 (21872) SS BOND : bond 0.00133 / 0.06 ( 7) SS BOND : angle 0.68315 / 0.33 ( 14) hydrogen bonds : bond 0.20689 / 13.89 ( 793) hydrogen bonds : angle 7.39515 / 5.22 ( 2537) link_ALPHA1-3 : bond 0.00121 / 0.06 ( 3) link_ALPHA1-3 : angle 0.71485 / 0.37 ( 9) link_ALPHA1-6 : bond 0.00141 / 0.07 ( 3) link_ALPHA1-6 : angle 0.54745 / 0.29 ( 9) link_BETA1-4 : bond 0.00225 / 0.12 ( 11) link_BETA1-4 : angle 1.19642 / 0.66 ( 33) link_NAG-ASN : bond 0.00186 / 0.09 ( 9) link_NAG-ASN : angle 1.55412 / 0.96 ( 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 : 0.474 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: 0.6271 time to fit residues: 295.0490 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 : 0.600 ------------------------------------------------------------------------------- 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... A 101 GLN A 149 ASN A 345 ASN B 243 ASN B 267 HIS C 267 HIS D 90 GLN D 267 HIS E 77 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062290 restraints weight = 64206.587| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.15 r_work: 0.2793 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (16 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16132 Z= 0.154 Angle : 0.659 14.141 21964 Z= 0.347 Chirality : 0.044 0.161 2510 Planarity : 0.005 0.068 2682 Dihedral : 5.166 55.507 2147 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.88 % Allowed : 14.17 % Favored : 82.95 % 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 : 0.77 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 96 TYR 0.024 0.002 TYR B 299 PHE 0.022 0.002 PHE C 306 TRP 0.035 0.001 TRP E 315 HIS 0.009 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16099) covalent geometry : angle 0.65511 / 0.35 (21872) SS BOND : bond 0.00212 / 0.10 ( 7) SS BOND : angle 0.43627 / 0.25 ( 14) hydrogen bonds : bond 0.04640 / 3.03 ( 793) hydrogen bonds : angle 5.11712 / 3.56 ( 2537) link_ALPHA1-3 : bond 0.00341 / 0.17 ( 3) link_ALPHA1-3 : angle 1.47922 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00335 / 0.17 ( 3) link_ALPHA1-6 : angle 1.49982 / 0.72 ( 9) link_BETA1-4 : bond 0.00235 / 0.13 ( 11) link_BETA1-4 : angle 1.41472 / 0.96 ( 33) link_NAG-ASN : bond 0.00193 / 0.09 ( 9) link_NAG-ASN : angle 1.41062 / 0.88 ( 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 : 0.418 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: 0.8698 (mtm) cc_final: 0.8366 (mmm) REVERT: A 92 GLU cc_start: 0.8563 (pt0) cc_final: 0.7953 (pm20) REVERT: A 260 MET cc_start: 0.8661 (tpp) cc_final: 0.8434 (tpp) REVERT: A 262 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8962 (mm-40) REVERT: A 321 TRP cc_start: 0.7704 (m-10) cc_final: 0.6856 (m100) REVERT: A 335 ILE cc_start: 0.9479 (mm) cc_final: 0.9274 (mm) REVERT: B 13 LYS cc_start: 0.8717 (tttt) cc_final: 0.8379 (ttpp) REVERT: B 52 GLU cc_start: 0.8856 (mp0) cc_final: 0.8649 (mp0) REVERT: B 215 LYS cc_start: 0.9271 (tttt) cc_final: 0.8950 (ttmm) REVERT: B 269 ARG cc_start: 0.8673 (ptm160) cc_final: 0.8371 (ptm160) REVERT: B 298 GLU cc_start: 0.9226 (tm-30) cc_final: 0.9022 (tm-30) REVERT: B 306 PHE cc_start: 0.8106 (t80) cc_final: 0.7530 (t80) REVERT: C 9 MET cc_start: 0.8523 (mtp) cc_final: 0.8039 (mtt) REVERT: C 90 GLN cc_start: 0.8997 (mp10) cc_final: 0.8135 (mp10) REVERT: C 278 VAL cc_start: 0.8598 (t) cc_final: 0.8367 (p) REVERT: C 286 MET cc_start: 0.9101 (mmp) cc_final: 0.8607 (mmm) REVERT: C 302 VAL cc_start: 0.9354 (t) cc_final: 0.9081 (t) REVERT: C 440 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9037 (tp) REVERT: D 13 LYS cc_start: 0.9187 (tttt) cc_final: 0.8530 (tmmt) REVERT: D 21 LYS cc_start: 0.8384 (mmmm) cc_final: 0.7996 (mmmm) REVERT: D 147 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 215 LYS cc_start: 0.9094 (tttt) cc_final: 0.8638 (tttp) REVERT: D 243 ASN cc_start: 0.8376 (t0) cc_final: 0.7997 (t0) REVERT: D 306 PHE cc_start: 0.7918 (t80) cc_final: 0.7292 (t80) REVERT: D 433 PHE cc_start: 0.8948 (t80) cc_final: 0.8715 (t80) REVERT: E 118 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8082 (mppt) REVERT: E 142 LYS cc_start: 0.9254 (mtmt) cc_final: 0.9017 (mtmm) REVERT: E 233 GLN cc_start: 0.8232 (tt0) cc_final: 0.7895 (tp40) REVERT: E 435 PHE cc_start: 0.8666 (m-80) cc_final: 0.8192 (m-80) REVERT: L 3 GLN cc_start: 0.8196 (mp10) cc_final: 0.7423 (mp10) REVERT: L 472 ASN cc_start: 0.8860 (t0) cc_final: 0.7977 (t0) REVERT: L 474 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8153 (mptm) REVERT: M 11 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7357 (tm) REVERT: M 472 ASN cc_start: 0.8773 (t0) cc_final: 0.8142 (t0) REVERT: M 473 LEU cc_start: 0.9407 (mt) cc_final: 0.9118 (mm) REVERT: M 474 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8296 (mmmt) outliers start: 48 outliers final: 10 residues processed: 308 average time/residue: 0.6154 time to fit residues: 207.3132 Evaluate side-chains 249 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 459 ARG 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: 0.9980 chunk 73 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 ASN C 267 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 227 ASN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 ASN L 504 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 = 0.3415 r_free = 0.3415 target = 0.082528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.060409 restraints weight = 53368.400| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.81 r_work: 0.2762 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16132 Z= 0.176 Angle : 0.624 10.000 21964 Z= 0.324 Chirality : 0.044 0.161 2510 Planarity : 0.004 0.038 2682 Dihedral : 5.009 57.793 2144 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.58 % Allowed : 14.23 % Favored : 83.19 % 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: 1.40 (0.20), residues: 1863 helix: 1.76 (0.21), residues: 569 sheet: 0.51 (0.23), residues: 497 loop : 0.77 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.026 0.002 TYR B 299 PHE 0.018 0.002 PHE D 306 TRP 0.022 0.001 TRP L 440 HIS 0.007 0.001 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (16099) covalent geometry : angle 0.61850 / 0.32 (21872) SS BOND : bond 0.00247 / 0.12 ( 7) SS BOND : angle 0.42592 / 0.24 ( 14) hydrogen bonds : bond 0.04056 / 2.62 ( 793) hydrogen bonds : angle 4.67871 / 3.22 ( 2537) link_ALPHA1-3 : bond 0.00352 / 0.18 ( 3) link_ALPHA1-3 : angle 1.41308 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00316 / 0.16 ( 3) link_ALPHA1-6 : angle 1.48394 / 0.72 ( 9) link_BETA1-4 : bond 0.00304 / 0.18 ( 11) link_BETA1-4 : angle 1.61595 / 1.05 ( 33) link_NAG-ASN : bond 0.00297 / 0.14 ( 9) link_NAG-ASN : angle 1.44707 / 0.95 ( 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 299 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 0.626 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: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8877 (ptt-90) cc_final: 0.8602 (ptt-90) REVERT: A 91 MET cc_start: 0.8763 (mtm) cc_final: 0.8373 (mmm) REVERT: A 92 GLU cc_start: 0.8592 (pt0) cc_final: 0.7982 (pm20) REVERT: A 321 TRP cc_start: 0.7701 (m-10) cc_final: 0.6812 (m100) REVERT: B 9 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7612 (mmt) REVERT: B 13 LYS cc_start: 0.8861 (tttt) cc_final: 0.8496 (ttpp) REVERT: B 18 LYS cc_start: 0.9265 (pttp) cc_final: 0.8941 (pptt) REVERT: B 215 LYS cc_start: 0.9260 (tttt) cc_final: 0.8932 (ttmm) REVERT: B 274 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8552 (tmtp) REVERT: B 278 VAL cc_start: 0.8373 (t) cc_final: 0.8022 (p) REVERT: B 306 PHE cc_start: 0.8093 (t80) cc_final: 0.7770 (t80) REVERT: C 9 MET cc_start: 0.8497 (mtp) cc_final: 0.8045 (mtt) REVERT: C 90 GLN cc_start: 0.8969 (mp10) cc_final: 0.8099 (mp10) REVERT: C 141 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8704 (mpp80) REVERT: C 230 ILE cc_start: 0.9677 (mt) cc_final: 0.9312 (mp) REVERT: D 13 LYS cc_start: 0.9198 (tttt) cc_final: 0.8540 (tmmt) REVERT: D 21 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8125 (mmmm) REVERT: D 147 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7710 (mm-30) REVERT: D 215 LYS cc_start: 0.9172 (tttt) cc_final: 0.8643 (tttp) REVERT: D 243 ASN cc_start: 0.8427 (t0) cc_final: 0.7919 (t0) REVERT: D 306 PHE cc_start: 0.7749 (t80) cc_final: 0.7484 (t80) REVERT: D 433 PHE cc_start: 0.8969 (t80) cc_final: 0.8717 (t80) REVERT: E 118 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8542 (mmtp) REVERT: E 224 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6698 (tm-30) REVERT: E 226 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7421 (ppp) REVERT: L 3 GLN cc_start: 0.8229 (mp10) cc_final: 0.7616 (mp10) REVERT: L 469 GLU cc_start: 0.8264 (mp0) cc_final: 0.8036 (mp0) REVERT: L 472 ASN cc_start: 0.8978 (t0) cc_final: 0.8476 (t0) REVERT: M 11 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7285 (tm) REVERT: M 472 ASN cc_start: 0.8961 (t0) cc_final: 0.8384 (t0) REVERT: M 473 LEU cc_start: 0.9417 (mt) cc_final: 0.8900 (mm) REVERT: M 474 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8396 (mmmt) REVERT: M 504 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8473 (pm20) outliers start: 43 outliers final: 11 residues processed: 280 average time/residue: 0.6935 time to fit residues: 212.0952 Evaluate side-chains 260 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 239 ILE Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain C residue 141 ARG 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 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 L residue 459 ARG 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: 6.9990 chunk 152 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 ASN B 243 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059865 restraints weight = 58883.767| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.94 r_work: 0.2747 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 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 = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16132 Z= 0.160 Angle : 0.614 11.309 21964 Z= 0.318 Chirality : 0.043 0.196 2510 Planarity : 0.004 0.066 2682 Dihedral : 4.970 59.630 2144 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.28 % Allowed : 15.55 % Favored : 82.17 % 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: 1.39 (0.20), residues: 1863 helix: 1.77 (0.21), residues: 569 sheet: 0.54 (0.23), residues: 507 loop : 0.73 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.027 0.002 TYR B 299 PHE 0.018 0.002 PHE C 293 TRP 0.020 0.001 TRP L 440 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16099) covalent geometry : angle 0.60900 / 0.32 (21872) SS BOND : bond 0.00167 / 0.09 ( 7) SS BOND : angle 0.38417 / 0.22 ( 14) hydrogen bonds : bond 0.03708 / 2.40 ( 793) hydrogen bonds : angle 4.53588 / 3.13 ( 2537) link_ALPHA1-3 : bond 0.00372 / 0.19 ( 3) link_ALPHA1-3 : angle 1.49219 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00355 / 0.18 ( 3) link_ALPHA1-6 : angle 1.52760 / 0.75 ( 9) link_BETA1-4 : bond 0.00273 / 0.16 ( 11) link_BETA1-4 : angle 1.56961 / 1.03 ( 33) link_NAG-ASN : bond 0.00065 / 0.03 ( 9) link_NAG-ASN : angle 1.45022 / 0.98 ( 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 292 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8739 (mtm) cc_final: 0.8515 (mtm) REVERT: A 92 GLU cc_start: 0.8614 (pt0) cc_final: 0.7985 (pm20) REVERT: A 321 TRP cc_start: 0.7673 (m-10) cc_final: 0.6775 (m100) REVERT: B 13 LYS cc_start: 0.8864 (tttt) cc_final: 0.8496 (ttpp) REVERT: B 18 LYS cc_start: 0.9256 (pttp) cc_final: 0.8969 (pptt) REVERT: B 52 GLU cc_start: 0.8950 (mp0) cc_final: 0.8671 (mp0) REVERT: B 147 GLU cc_start: 0.8756 (tt0) cc_final: 0.8520 (tt0) REVERT: B 190 GLU cc_start: 0.8871 (tt0) cc_final: 0.8248 (pt0) REVERT: B 215 LYS cc_start: 0.9292 (tttt) cc_final: 0.8968 (ttmm) REVERT: B 274 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8590 (tmtp) REVERT: B 278 VAL cc_start: 0.8463 (t) cc_final: 0.8169 (p) REVERT: C 9 MET cc_start: 0.8495 (mtp) cc_final: 0.8116 (ttm) REVERT: C 90 GLN cc_start: 0.8963 (mp10) cc_final: 0.8096 (mp10) REVERT: C 424 ASP cc_start: 0.9172 (m-30) cc_final: 0.8870 (m-30) REVERT: D 9 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8051 (tpt) REVERT: D 13 LYS cc_start: 0.9207 (tttt) cc_final: 0.8450 (tmmt) REVERT: D 21 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8291 (mmmm) REVERT: D 102 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9026 (mtmt) REVERT: D 147 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7594 (mm-30) REVERT: D 215 LYS cc_start: 0.9183 (tttt) cc_final: 0.8700 (ttmm) REVERT: D 243 ASN cc_start: 0.8427 (t0) cc_final: 0.7882 (t0) REVERT: D 306 PHE cc_start: 0.7775 (t80) cc_final: 0.7544 (t80) REVERT: D 433 PHE cc_start: 0.8980 (t80) cc_final: 0.8722 (t80) REVERT: E 118 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8157 (mppt) REVERT: E 142 LYS cc_start: 0.9214 (mtmt) cc_final: 0.9008 (mtmm) REVERT: E 179 MET cc_start: 0.8817 (mpp) cc_final: 0.8517 (tpp) REVERT: E 213 GLN cc_start: 0.8703 (tt0) cc_final: 0.8437 (tt0) REVERT: E 224 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: L 3 GLN cc_start: 0.8430 (mp-120) cc_final: 0.7604 (mp10) REVERT: L 469 GLU cc_start: 0.8201 (mp0) cc_final: 0.7969 (mp0) REVERT: L 472 ASN cc_start: 0.8977 (t0) cc_final: 0.8460 (t0) REVERT: M 11 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7267 (tm) REVERT: M 459 ARG cc_start: 0.8167 (pmt170) cc_final: 0.7832 (pmt-80) REVERT: M 467 TYR cc_start: 0.8435 (m-80) cc_final: 0.8087 (m-80) REVERT: M 469 GLU cc_start: 0.8599 (mp0) cc_final: 0.7690 (mp0) REVERT: M 472 ASN cc_start: 0.9019 (t0) cc_final: 0.8343 (t0) REVERT: M 473 LEU cc_start: 0.9406 (mt) cc_final: 0.9075 (mm) REVERT: M 474 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8279 (mmpt) outliers start: 38 outliers final: 16 residues processed: 277 average time/residue: 0.7059 time to fit residues: 213.5294 Evaluate side-chains 260 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 256 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 115 MET 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 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 L residue 459 ARG 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: 5.9990 chunk 2 optimal weight: 0.0970 chunk 184 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN 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 ** 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 = 0.3414 r_free = 0.3414 target = 0.082411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061095 restraints weight = 41867.303| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.39 r_work: 0.2792 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16132 Z= 0.142 Angle : 0.613 14.328 21964 Z= 0.313 Chirality : 0.043 0.172 2510 Planarity : 0.004 0.063 2682 Dihedral : 4.878 56.538 2144 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.58 % Allowed : 16.09 % Favored : 81.33 % 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: 1.46 (0.20), residues: 1863 helix: 1.82 (0.21), residues: 569 sheet: 0.61 (0.23), residues: 507 loop : 0.75 (0.24), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 307 TYR 0.025 0.001 TYR B 299 PHE 0.018 0.001 PHE C 293 TRP 0.021 0.001 TRP L 440 HIS 0.002 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16099) covalent geometry : angle 0.60791 / 0.31 (21872) SS BOND : bond 0.00113 / 0.06 ( 7) SS BOND : angle 0.45890 / 0.27 ( 14) hydrogen bonds : bond 0.03573 / 2.30 ( 793) hydrogen bonds : angle 4.43563 / 3.05 ( 2537) link_ALPHA1-3 : bond 0.00334 / 0.17 ( 3) link_ALPHA1-3 : angle 1.46897 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00342 / 0.17 ( 3) link_ALPHA1-6 : angle 1.48746 / 0.73 ( 9) link_BETA1-4 : bond 0.00298 / 0.18 ( 11) link_BETA1-4 : angle 1.51829 / 0.99 ( 33) link_NAG-ASN : bond 0.00066 / 0.03 ( 9) link_NAG-ASN : angle 1.38964 / 0.93 ( 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 300 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.440 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: 0.8713 (mtm) cc_final: 0.8330 (mmm) REVERT: A 92 GLU cc_start: 0.8569 (pt0) cc_final: 0.7975 (pm20) REVERT: A 262 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8838 (mt0) REVERT: A 321 TRP cc_start: 0.7660 (m-10) cc_final: 0.6768 (m100) REVERT: B 13 LYS cc_start: 0.8896 (tttt) cc_final: 0.8521 (ttpp) REVERT: B 18 LYS cc_start: 0.9248 (pttp) cc_final: 0.8971 (pptt) REVERT: B 49 MET cc_start: 0.8883 (ttp) cc_final: 0.8140 (tmm) REVERT: B 52 GLU cc_start: 0.8874 (mp0) cc_final: 0.8647 (mp0) REVERT: B 147 GLU cc_start: 0.8689 (tt0) cc_final: 0.8418 (tt0) REVERT: B 190 GLU cc_start: 0.8850 (tt0) cc_final: 0.8505 (pt0) REVERT: B 215 LYS cc_start: 0.9267 (tttt) cc_final: 0.8918 (ttmm) REVERT: B 274 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8716 (ttmm) REVERT: B 278 VAL cc_start: 0.8441 (t) cc_final: 0.8191 (p) REVERT: B 298 GLU cc_start: 0.9264 (tm-30) cc_final: 0.9024 (tm-30) REVERT: C 9 MET cc_start: 0.8475 (mtp) cc_final: 0.8120 (ttm) REVERT: C 90 GLN cc_start: 0.8947 (mp10) cc_final: 0.8032 (mp10) REVERT: C 141 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8720 (mpp80) REVERT: C 244 TYR cc_start: 0.8814 (p90) cc_final: 0.8603 (p90) REVERT: C 424 ASP cc_start: 0.9130 (m-30) cc_final: 0.8808 (m-30) REVERT: D 13 LYS cc_start: 0.9169 (tttt) cc_final: 0.8540 (tmmt) REVERT: D 21 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8363 (mmmm) REVERT: D 147 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7619 (mm-30) REVERT: D 215 LYS cc_start: 0.9203 (tttt) cc_final: 0.8754 (ttmm) REVERT: D 243 ASN cc_start: 0.8441 (t0) cc_final: 0.7927 (t0) REVERT: D 306 PHE cc_start: 0.7724 (t80) cc_final: 0.7494 (t80) REVERT: D 426 TRP cc_start: 0.8685 (m100) cc_final: 0.8425 (t-100) REVERT: D 433 PHE cc_start: 0.8968 (t80) cc_final: 0.8709 (t80) REVERT: E 118 LYS cc_start: 0.9005 (mmtm) cc_final: 0.8201 (mppt) REVERT: E 142 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8965 (mtmm) REVERT: E 179 MET cc_start: 0.8692 (mpp) cc_final: 0.8374 (tpp) REVERT: E 213 GLN cc_start: 0.8808 (tt0) cc_final: 0.8552 (tt0) REVERT: E 224 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: E 226 MET cc_start: 0.8080 (ppp) cc_final: 0.7715 (ppp) REVERT: E 253 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7795 (pp30) REVERT: E 313 TYR cc_start: 0.9372 (t80) cc_final: 0.9048 (t80) REVERT: L 3 GLN cc_start: 0.8413 (mp-120) cc_final: 0.7701 (mp10) REVERT: L 407 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8291 (mt) REVERT: L 469 GLU cc_start: 0.8212 (mp0) cc_final: 0.7937 (mp0) REVERT: L 472 ASN cc_start: 0.9044 (t0) cc_final: 0.8601 (t0) REVERT: M 11 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7371 (tm) REVERT: M 459 ARG cc_start: 0.8162 (pmt170) cc_final: 0.7745 (pmt-80) REVERT: M 467 TYR cc_start: 0.8488 (m-80) cc_final: 0.8053 (m-80) REVERT: M 469 GLU cc_start: 0.8605 (mp0) cc_final: 0.7760 (mp0) REVERT: M 472 ASN cc_start: 0.9045 (t0) cc_final: 0.8711 (t0) REVERT: M 473 LEU cc_start: 0.9347 (mt) cc_final: 0.8717 (mm) REVERT: M 474 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8333 (mmmt) outliers start: 43 outliers final: 18 residues processed: 283 average time/residue: 0.6380 time to fit residues: 197.2327 Evaluate side-chains 266 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 269 ARG Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 16 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 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 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 460 ASP 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: 6.9990 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN 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** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.059294 restraints weight = 67131.844| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.16 r_work: 0.2727 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16132 Z= 0.166 Angle : 0.629 12.019 21964 Z= 0.320 Chirality : 0.043 0.193 2510 Planarity : 0.004 0.061 2682 Dihedral : 4.443 19.504 2140 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.58 % Allowed : 16.21 % Favored : 81.21 % 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: 1.46 (0.20), residues: 1863 helix: 1.82 (0.21), residues: 569 sheet: 0.66 (0.23), residues: 507 loop : 0.73 (0.24), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 307 TYR 0.033 0.002 TYR D 220 PHE 0.025 0.001 PHE C 293 TRP 0.023 0.001 TRP L 440 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (16099) covalent geometry : angle 0.62330 / 0.32 (21872) SS BOND : bond 0.00107 / 0.07 ( 7) SS BOND : angle 0.48600 / 0.28 ( 14) hydrogen bonds : bond 0.03583 / 2.32 ( 793) hydrogen bonds : angle 4.42355 / 3.04 ( 2537) link_ALPHA1-3 : bond 0.00292 / 0.15 ( 3) link_ALPHA1-3 : angle 1.48184 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00303 / 0.16 ( 3) link_ALPHA1-6 : angle 1.52692 / 0.75 ( 9) link_BETA1-4 : bond 0.00273 / 0.16 ( 11) link_BETA1-4 : angle 1.58348 / 1.03 ( 33) link_NAG-ASN : bond 0.00063 / 0.03 ( 9) link_NAG-ASN : angle 1.39905 / 0.93 ( 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 299 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 0.558 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: 0.8760 (mtm) cc_final: 0.8380 (mmm) REVERT: A 92 GLU cc_start: 0.8626 (pt0) cc_final: 0.7996 (pm20) REVERT: A 181 MET cc_start: 0.8730 (mtm) cc_final: 0.8517 (pmm) REVERT: A 262 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8939 (mt0) REVERT: A 267 CYS cc_start: 0.9222 (m) cc_final: 0.8953 (m) REVERT: A 321 TRP cc_start: 0.7736 (m-10) cc_final: 0.6846 (m100) REVERT: B 13 LYS cc_start: 0.8888 (tttt) cc_final: 0.8530 (ttpp) REVERT: B 18 LYS cc_start: 0.9270 (pttp) cc_final: 0.8971 (pptt) REVERT: B 49 MET cc_start: 0.8955 (ttp) cc_final: 0.8194 (tmm) REVERT: B 52 GLU cc_start: 0.9001 (mp0) cc_final: 0.8795 (mp0) REVERT: B 70 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.8958 (mmtm) REVERT: B 147 GLU cc_start: 0.8763 (tt0) cc_final: 0.8497 (tt0) REVERT: B 190 GLU cc_start: 0.8919 (tt0) cc_final: 0.8600 (pt0) REVERT: B 215 LYS cc_start: 0.9314 (tttt) cc_final: 0.8971 (ttmm) REVERT: B 269 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8474 (ttt90) REVERT: B 274 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8714 (ttmm) REVERT: B 278 VAL cc_start: 0.8552 (t) cc_final: 0.8345 (p) REVERT: B 298 GLU cc_start: 0.9307 (tm-30) cc_final: 0.8976 (tm-30) REVERT: B 302 VAL cc_start: 0.9384 (t) cc_final: 0.9165 (t) REVERT: C 9 MET cc_start: 0.8485 (mtp) cc_final: 0.8106 (ttm) REVERT: C 90 GLN cc_start: 0.8910 (mp10) cc_final: 0.7968 (mp10) REVERT: C 141 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8724 (mpp80) REVERT: C 244 TYR cc_start: 0.8861 (p90) cc_final: 0.8605 (p90) REVERT: C 424 ASP cc_start: 0.9153 (m-30) cc_final: 0.8825 (m-30) REVERT: D 13 LYS cc_start: 0.9113 (tttt) cc_final: 0.8505 (tmmt) REVERT: D 21 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8406 (mmmm) REVERT: D 147 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 215 LYS cc_start: 0.9227 (tttt) cc_final: 0.8688 (ttmm) REVERT: D 243 ASN cc_start: 0.8466 (t0) cc_final: 0.7953 (t0) REVERT: D 426 TRP cc_start: 0.8707 (m100) cc_final: 0.8462 (t-100) REVERT: D 433 PHE cc_start: 0.8989 (t80) cc_final: 0.8735 (t80) REVERT: E 118 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8290 (mppt) REVERT: E 142 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8990 (mtmm) REVERT: E 179 MET cc_start: 0.8754 (mpp) cc_final: 0.8447 (tpp) REVERT: E 213 GLN cc_start: 0.8811 (tt0) cc_final: 0.8505 (tt0) REVERT: E 224 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: E 313 TYR cc_start: 0.9396 (t80) cc_final: 0.9104 (t80) REVERT: L 1 GLN cc_start: 0.6653 (tm-30) cc_final: 0.6374 (pp30) REVERT: L 3 GLN cc_start: 0.8479 (mp-120) cc_final: 0.8002 (mp10) REVERT: L 407 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8267 (mt) REVERT: L 430 LYS cc_start: 0.8921 (mppt) cc_final: 0.8474 (mptt) REVERT: L 469 GLU cc_start: 0.8249 (mp0) cc_final: 0.8002 (mp0) REVERT: L 472 ASN cc_start: 0.9091 (t0) cc_final: 0.8635 (t0) REVERT: M 11 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7482 (tm) REVERT: M 464 ASN cc_start: 0.8954 (m-40) cc_final: 0.8702 (p0) REVERT: M 467 TYR cc_start: 0.8526 (m-80) cc_final: 0.8043 (m-80) REVERT: M 469 GLU cc_start: 0.8561 (mp0) cc_final: 0.7683 (mp0) REVERT: M 472 ASN cc_start: 0.9080 (t0) cc_final: 0.8416 (t0) REVERT: M 473 LEU cc_start: 0.9284 (mt) cc_final: 0.8968 (mm) REVERT: M 474 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8260 (mmpt) outliers start: 43 outliers final: 18 residues processed: 281 average time/residue: 0.6404 time to fit residues: 196.7536 Evaluate side-chains 260 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 70 LYS Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 141 ARG 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 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 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 460 ASP 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: 2.9990 chunk 85 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN A 345 ASN ** 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 = 0.3424 r_free = 0.3424 target = 0.082854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060321 restraints weight = 66336.383| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.17 r_work: 0.2753 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16132 Z= 0.131 Angle : 0.626 13.196 21964 Z= 0.317 Chirality : 0.043 0.193 2510 Planarity : 0.003 0.048 2682 Dihedral : 4.388 27.453 2140 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.28 % Allowed : 17.05 % Favored : 80.67 % 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: 1.47 (0.20), residues: 1863 helix: 1.81 (0.21), residues: 570 sheet: 0.71 (0.23), residues: 507 loop : 0.71 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 307 TYR 0.026 0.001 TYR B 299 PHE 0.023 0.001 PHE B 306 TRP 0.027 0.001 TRP L 440 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (16099) covalent geometry : angle 0.62104 / 0.32 (21872) SS BOND : bond 0.00077 / 0.04 ( 7) SS BOND : angle 0.50437 / 0.29 ( 14) hydrogen bonds : bond 0.03479 / 2.25 ( 793) hydrogen bonds : angle 4.38074 / 3.00 ( 2537) link_ALPHA1-3 : bond 0.00318 / 0.16 ( 3) link_ALPHA1-3 : angle 1.45936 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00340 / 0.17 ( 3) link_ALPHA1-6 : angle 1.48100 / 0.72 ( 9) link_BETA1-4 : bond 0.00277 / 0.16 ( 11) link_BETA1-4 : angle 1.47327 / 0.97 ( 33) link_NAG-ASN : bond 0.00082 / 0.04 ( 9) link_NAG-ASN : angle 1.31953 / 0.89 ( 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 288 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.612 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: 0.8789 (mtm) cc_final: 0.8439 (mmm) REVERT: A 92 GLU cc_start: 0.8620 (pt0) cc_final: 0.8020 (pm20) REVERT: A 181 MET cc_start: 0.8758 (mtm) cc_final: 0.8483 (pmm) REVERT: A 256 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7944 (pmm) REVERT: A 262 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8931 (mt0) REVERT: A 267 CYS cc_start: 0.9227 (m) cc_final: 0.8971 (m) REVERT: A 282 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8634 (ptpp) REVERT: A 321 TRP cc_start: 0.7676 (m-10) cc_final: 0.6821 (m100) REVERT: B 49 MET cc_start: 0.8903 (ttp) cc_final: 0.8252 (tmm) REVERT: B 70 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.8971 (mmtm) REVERT: B 147 GLU cc_start: 0.8748 (tt0) cc_final: 0.8470 (tt0) REVERT: B 190 GLU cc_start: 0.8902 (tt0) cc_final: 0.8590 (pt0) REVERT: B 274 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8715 (ttmm) REVERT: B 298 GLU cc_start: 0.9321 (tm-30) cc_final: 0.8986 (tm-30) REVERT: B 302 VAL cc_start: 0.9402 (t) cc_final: 0.9194 (t) REVERT: C 9 MET cc_start: 0.8495 (mtp) cc_final: 0.8114 (ttm) REVERT: C 90 GLN cc_start: 0.8925 (mp10) cc_final: 0.8010 (mp10) REVERT: C 141 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8748 (mpp80) REVERT: C 244 TYR cc_start: 0.8851 (p90) cc_final: 0.8602 (p90) REVERT: C 297 LEU cc_start: 0.9422 (mp) cc_final: 0.9149 (mp) REVERT: C 424 ASP cc_start: 0.9094 (m-30) cc_final: 0.8746 (m-30) REVERT: D 13 LYS cc_start: 0.9139 (tttt) cc_final: 0.8516 (tmmt) REVERT: D 21 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8417 (mmmm) REVERT: D 147 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7814 (mm-30) REVERT: D 215 LYS cc_start: 0.9217 (tttt) cc_final: 0.8690 (ttmm) REVERT: D 243 ASN cc_start: 0.8450 (t0) cc_final: 0.7905 (t0) REVERT: D 426 TRP cc_start: 0.8673 (m100) cc_final: 0.8442 (t-100) REVERT: D 433 PHE cc_start: 0.8986 (t80) cc_final: 0.8735 (t80) REVERT: E 82 ASN cc_start: 0.9211 (m-40) cc_final: 0.8912 (m-40) REVERT: E 118 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8343 (mppt) REVERT: E 179 MET cc_start: 0.8700 (mpp) cc_final: 0.8432 (tpp) REVERT: E 213 GLN cc_start: 0.8820 (tt0) cc_final: 0.8494 (tt0) REVERT: E 224 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: E 253 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7936 (pp30) REVERT: E 313 TYR cc_start: 0.9427 (t80) cc_final: 0.9099 (t80) REVERT: L 1 GLN cc_start: 0.6683 (tm-30) cc_final: 0.6469 (pp30) REVERT: L 3 GLN cc_start: 0.8579 (mp-120) cc_final: 0.8095 (mp10) REVERT: L 407 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8313 (mt) REVERT: L 469 GLU cc_start: 0.8225 (mp0) cc_final: 0.7907 (mp0) REVERT: L 472 ASN cc_start: 0.9141 (t0) cc_final: 0.8709 (t0) REVERT: M 11 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7538 (tm) REVERT: M 430 LYS cc_start: 0.8782 (ptpp) cc_final: 0.8566 (mppt) REVERT: M 464 ASN cc_start: 0.8937 (m110) cc_final: 0.8688 (p0) REVERT: M 467 TYR cc_start: 0.8614 (m-80) cc_final: 0.8052 (m-80) REVERT: M 469 GLU cc_start: 0.8562 (mp0) cc_final: 0.7719 (mp0) REVERT: M 472 ASN cc_start: 0.9085 (t0) cc_final: 0.8657 (t0) outliers start: 38 outliers final: 14 residues processed: 273 average time/residue: 0.6885 time to fit residues: 205.5646 Evaluate side-chains 258 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 132 THR 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 278 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 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 11 LEU Chi-restraints excluded: chain L residue 407 LEU 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: 10.0000 chunk 130 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3418 r_free = 0.3418 target = 0.082685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.060259 restraints weight = 58964.024| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.93 r_work: 0.2755 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16132 Z= 0.172 Angle : 0.647 9.191 21964 Z= 0.329 Chirality : 0.044 0.191 2510 Planarity : 0.003 0.053 2682 Dihedral : 4.410 25.934 2140 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.22 % Allowed : 17.53 % Favored : 80.25 % 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: 1.42 (0.20), residues: 1863 helix: 1.75 (0.21), residues: 570 sheet: 0.77 (0.23), residues: 501 loop : 0.63 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 307 TYR 0.027 0.002 TYR B 299 PHE 0.021 0.002 PHE D 306 TRP 0.021 0.001 TRP L 440 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (16099) covalent geometry : angle 0.64163 / 0.33 (21872) SS BOND : bond 0.00137 / 0.09 ( 7) SS BOND : angle 0.48254 / 0.30 ( 14) hydrogen bonds : bond 0.03548 / 2.30 ( 793) hydrogen bonds : angle 4.44319 / 3.06 ( 2537) link_ALPHA1-3 : bond 0.00289 / 0.15 ( 3) link_ALPHA1-3 : angle 1.50394 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00269 / 0.14 ( 3) link_ALPHA1-6 : angle 1.53957 / 0.75 ( 9) link_BETA1-4 : bond 0.00269 / 0.16 ( 11) link_BETA1-4 : angle 1.59092 / 1.03 ( 33) link_NAG-ASN : bond 0.00070 / 0.03 ( 9) link_NAG-ASN : angle 1.35757 / 0.91 ( 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 284 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.680 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: 0.8817 (mtm) cc_final: 0.8400 (mmm) REVERT: A 92 GLU cc_start: 0.8610 (pt0) cc_final: 0.8045 (pm20) REVERT: A 181 MET cc_start: 0.8734 (mtm) cc_final: 0.8512 (pmm) REVERT: A 256 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7920 (pmm) REVERT: A 267 CYS cc_start: 0.9217 (m) cc_final: 0.8953 (m) REVERT: A 282 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8614 (ptpp) REVERT: A 321 TRP cc_start: 0.7714 (m-10) cc_final: 0.6806 (m100) REVERT: B 49 MET cc_start: 0.8818 (ttp) cc_final: 0.8001 (pp-130) REVERT: B 70 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9000 (mmtm) REVERT: B 147 GLU cc_start: 0.8723 (tt0) cc_final: 0.8441 (tt0) REVERT: B 190 GLU cc_start: 0.8874 (tt0) cc_final: 0.8608 (pt0) REVERT: C 9 MET cc_start: 0.8500 (mtp) cc_final: 0.8111 (ttm) REVERT: C 90 GLN cc_start: 0.8895 (mp10) cc_final: 0.7969 (mp10) REVERT: C 244 TYR cc_start: 0.8864 (p90) cc_final: 0.8587 (p90) REVERT: C 297 LEU cc_start: 0.9454 (mp) cc_final: 0.9195 (mp) REVERT: C 424 ASP cc_start: 0.9094 (m-30) cc_final: 0.8759 (m-30) REVERT: D 13 LYS cc_start: 0.9142 (tttt) cc_final: 0.8516 (tmmt) REVERT: D 147 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7763 (mm-30) REVERT: D 215 LYS cc_start: 0.9236 (tttt) cc_final: 0.8684 (ttmm) REVERT: D 243 ASN cc_start: 0.8453 (t0) cc_final: 0.7878 (t0) REVERT: D 274 LYS cc_start: 0.9003 (mttt) cc_final: 0.8705 (mmtt) REVERT: D 426 TRP cc_start: 0.8665 (m100) cc_final: 0.8438 (t-100) REVERT: D 433 PHE cc_start: 0.8983 (t80) cc_final: 0.8733 (t80) REVERT: E 82 ASN cc_start: 0.9135 (m-40) cc_final: 0.8833 (m-40) REVERT: E 118 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8394 (mppt) REVERT: E 179 MET cc_start: 0.8712 (mpp) cc_final: 0.8441 (tpp) REVERT: E 213 GLN cc_start: 0.8818 (tt0) cc_final: 0.8496 (tt0) REVERT: E 224 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: E 226 MET cc_start: 0.7924 (ppp) cc_final: 0.7705 (ppp) REVERT: E 228 PHE cc_start: 0.8567 (m-80) cc_final: 0.8286 (m-80) REVERT: E 253 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7889 (pp30) REVERT: E 313 TYR cc_start: 0.9424 (t80) cc_final: 0.9069 (t80) REVERT: L 1 GLN cc_start: 0.6733 (tm-30) cc_final: 0.6514 (pp30) REVERT: L 3 GLN cc_start: 0.8559 (mp-120) cc_final: 0.8092 (mp10) REVERT: L 464 ASN cc_start: 0.8854 (p0) cc_final: 0.8129 (p0) REVERT: L 469 GLU cc_start: 0.8218 (mp0) cc_final: 0.7872 (mp0) REVERT: L 472 ASN cc_start: 0.9171 (t0) cc_final: 0.8755 (t0) REVERT: M 11 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7587 (tm) REVERT: M 464 ASN cc_start: 0.8939 (m110) cc_final: 0.8735 (p0) REVERT: M 467 TYR cc_start: 0.8577 (m-80) cc_final: 0.8005 (m-80) REVERT: M 469 GLU cc_start: 0.8608 (mp0) cc_final: 0.7757 (mp0) REVERT: M 472 ASN cc_start: 0.9097 (t0) cc_final: 0.8599 (t0) outliers start: 37 outliers final: 19 residues processed: 271 average time/residue: 0.6749 time to fit residues: 200.1707 Evaluate side-chains 258 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 256 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 440 LEU 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 165 GLU 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 440 LEU Chi-restraints excluded: chain D residue 444 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 11 LEU 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: 7.9990 chunk 72 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060955 restraints weight = 46170.739| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.46 r_work: 0.2780 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- 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 = 0.26 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16132 Z= 0.170 Angle : 0.676 12.562 21964 Z= 0.342 Chirality : 0.044 0.193 2510 Planarity : 0.003 0.055 2682 Dihedral : 4.429 24.780 2140 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.16 % Allowed : 18.07 % Favored : 79.77 % 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: 1.69 (0.21), residues: 570 sheet: 0.72 (0.23), residues: 504 loop : 0.61 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 307 TYR 0.028 0.002 TYR D 220 PHE 0.018 0.001 PHE C 293 TRP 0.017 0.001 TRP L 440 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16099) covalent geometry : angle 0.67087 / 0.34 (21872) SS BOND : bond 0.00104 / 0.07 ( 7) SS BOND : angle 0.53251 / 0.32 ( 14) hydrogen bonds : bond 0.03573 / 2.33 ( 793) hydrogen bonds : angle 4.49033 / 3.09 ( 2537) link_ALPHA1-3 : bond 0.00278 / 0.14 ( 3) link_ALPHA1-3 : angle 1.50722 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00252 / 0.13 ( 3) link_ALPHA1-6 : angle 1.54456 / 0.75 ( 9) link_BETA1-4 : bond 0.00275 / 0.16 ( 11) link_BETA1-4 : angle 1.58655 / 1.03 ( 33) link_NAG-ASN : bond 0.00079 / 0.04 ( 9) link_NAG-ASN : angle 1.36596 / 0.92 ( 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 284 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.555 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: 0.8410 (mmm) REVERT: A 92 GLU cc_start: 0.8582 (pt0) cc_final: 0.8030 (pm20) REVERT: A 160 ILE cc_start: 0.9371 (mt) cc_final: 0.9145 (mp) REVERT: A 181 MET cc_start: 0.8706 (mtm) cc_final: 0.8504 (pmm) REVERT: A 260 MET cc_start: 0.8164 (mpp) cc_final: 0.7954 (mpt) REVERT: A 262 GLN cc_start: 0.9043 (mt0) cc_final: 0.8753 (mt0) REVERT: A 267 CYS cc_start: 0.9176 (m) cc_final: 0.8926 (m) REVERT: A 282 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8624 (ptpp) REVERT: A 321 TRP cc_start: 0.7679 (m-10) cc_final: 0.6780 (m100) REVERT: B 13 LYS cc_start: 0.8984 (tttt) cc_final: 0.8611 (ttpp) REVERT: B 18 LYS cc_start: 0.9260 (pttp) cc_final: 0.8871 (pptt) REVERT: B 49 MET cc_start: 0.8768 (ttp) cc_final: 0.7971 (pp-130) REVERT: B 70 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8996 (mmtm) REVERT: B 147 GLU cc_start: 0.8686 (tt0) cc_final: 0.8408 (tt0) REVERT: B 190 GLU cc_start: 0.8836 (tt0) cc_final: 0.8557 (pt0) REVERT: C 9 MET cc_start: 0.8463 (mtp) cc_final: 0.8079 (ttm) REVERT: C 84 ASP cc_start: 0.8448 (t70) cc_final: 0.7955 (t70) REVERT: C 90 GLN cc_start: 0.8901 (mp10) cc_final: 0.7987 (mp10) REVERT: C 244 TYR cc_start: 0.8853 (p90) cc_final: 0.8580 (p90) REVERT: C 297 LEU cc_start: 0.9457 (mp) cc_final: 0.9220 (mp) REVERT: C 424 ASP cc_start: 0.9045 (m-30) cc_final: 0.8725 (m-30) REVERT: D 13 LYS cc_start: 0.9169 (tttt) cc_final: 0.8537 (tmmt) REVERT: D 21 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8319 (mtmm) REVERT: D 147 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7733 (mm-30) REVERT: D 190 GLU cc_start: 0.8588 (tt0) cc_final: 0.8249 (tt0) REVERT: D 215 LYS cc_start: 0.9230 (tttt) cc_final: 0.8683 (ttmm) REVERT: D 243 ASN cc_start: 0.8466 (t0) cc_final: 0.7932 (t0) REVERT: D 274 LYS cc_start: 0.8967 (mttt) cc_final: 0.8682 (mmtt) REVERT: D 426 TRP cc_start: 0.8668 (m100) cc_final: 0.8442 (t-100) REVERT: D 433 PHE cc_start: 0.8957 (t80) cc_final: 0.8733 (t80) REVERT: E 82 ASN cc_start: 0.9171 (m-40) cc_final: 0.8853 (m-40) REVERT: E 118 LYS cc_start: 0.9119 (mmtm) cc_final: 0.8369 (mppt) REVERT: E 179 MET cc_start: 0.8683 (mpp) cc_final: 0.8424 (tpp) REVERT: E 213 GLN cc_start: 0.8817 (tt0) cc_final: 0.8503 (tt0) REVERT: E 224 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6345 (tm-30) REVERT: E 253 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7758 (pp30) REVERT: E 313 TYR cc_start: 0.9409 (t80) cc_final: 0.9003 (t80) REVERT: L 1 GLN cc_start: 0.6730 (tm-30) cc_final: 0.6519 (pp30) REVERT: L 3 GLN cc_start: 0.8517 (mp-120) cc_final: 0.8111 (mp10) REVERT: L 464 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8256 (p0) REVERT: L 469 GLU cc_start: 0.8195 (mp0) cc_final: 0.7929 (mp0) REVERT: L 472 ASN cc_start: 0.9236 (t0) cc_final: 0.8830 (t0) REVERT: L 476 GLU cc_start: 0.8545 (mp0) cc_final: 0.8301 (pm20) REVERT: M 11 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7609 (tm) REVERT: M 467 TYR cc_start: 0.8537 (m-80) cc_final: 0.7936 (m-80) REVERT: M 469 GLU cc_start: 0.8600 (mp0) cc_final: 0.7748 (mp0) REVERT: M 472 ASN cc_start: 0.9104 (t0) cc_final: 0.8604 (t0) outliers start: 36 outliers final: 15 residues processed: 271 average time/residue: 0.6448 time to fit residues: 191.0004 Evaluate side-chains 261 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 440 LEU 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 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 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 11 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 464 ASN 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: 0.9990 chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060628 restraints weight = 58834.538| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.86 r_work: 0.2759 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16132 Z= 0.155 Angle : 0.682 15.730 21964 Z= 0.344 Chirality : 0.044 0.207 2510 Planarity : 0.003 0.057 2682 Dihedral : 4.425 23.882 2140 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 1.34 (0.20), residues: 1863 helix: 1.68 (0.21), residues: 569 sheet: 0.71 (0.24), residues: 504 loop : 0.58 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 307 TYR 0.026 0.002 TYR B 299 PHE 0.022 0.001 PHE D 306 TRP 0.020 0.001 TRP L 440 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (16099) covalent geometry : angle 0.67808 / 0.34 (21872) SS BOND : bond 0.00089 / 0.04 ( 7) SS BOND : angle 0.59804 / 0.39 ( 14) hydrogen bonds : bond 0.03566 / 2.33 ( 793) hydrogen bonds : angle 4.48392 / 3.09 ( 2537) link_ALPHA1-3 : bond 0.00282 / 0.14 ( 3) link_ALPHA1-3 : angle 1.49123 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00263 / 0.14 ( 3) link_ALPHA1-6 : angle 1.52188 / 0.74 ( 9) link_BETA1-4 : bond 0.00268 / 0.15 ( 11) link_BETA1-4 : angle 1.53506 / 1.00 ( 33) link_NAG-ASN : bond 0.00073 / 0.04 ( 9) link_NAG-ASN : angle 1.34179 / 0.90 ( 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 272 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.495 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: 0.8846 (mtm) cc_final: 0.8443 (mmm) REVERT: A 92 GLU cc_start: 0.8635 (pt0) cc_final: 0.8070 (pm20) REVERT: A 160 ILE cc_start: 0.9379 (mt) cc_final: 0.9164 (mp) REVERT: A 181 MET cc_start: 0.8718 (mtm) cc_final: 0.8486 (pmm) REVERT: A 262 GLN cc_start: 0.9017 (mt0) cc_final: 0.8810 (mt0) REVERT: A 267 CYS cc_start: 0.9193 (m) cc_final: 0.8931 (m) REVERT: A 282 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8606 (ptpp) REVERT: A 321 TRP cc_start: 0.7726 (m-10) cc_final: 0.6832 (m100) REVERT: B 49 MET cc_start: 0.8796 (ttp) cc_final: 0.8010 (pp-130) REVERT: B 70 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9015 (mmtm) REVERT: B 147 GLU cc_start: 0.8715 (tt0) cc_final: 0.8436 (tt0) REVERT: B 190 GLU cc_start: 0.8856 (tt0) cc_final: 0.8578 (pt0) REVERT: B 274 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8717 (ttmm) REVERT: B 306 PHE cc_start: 0.7544 (t80) cc_final: 0.7341 (t80) REVERT: C 9 MET cc_start: 0.8443 (mtp) cc_final: 0.8016 (ttm) REVERT: C 84 ASP cc_start: 0.8459 (t70) cc_final: 0.7956 (t70) REVERT: C 90 GLN cc_start: 0.8887 (mp10) cc_final: 0.7969 (mp10) REVERT: C 244 TYR cc_start: 0.8872 (p90) cc_final: 0.8603 (p90) REVERT: C 297 LEU cc_start: 0.9477 (mp) cc_final: 0.9272 (mp) REVERT: C 424 ASP cc_start: 0.9037 (m-30) cc_final: 0.8733 (m-30) REVERT: D 13 LYS cc_start: 0.9141 (tttt) cc_final: 0.8509 (tmmt) REVERT: D 147 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7854 (mm-30) REVERT: D 190 GLU cc_start: 0.8638 (tt0) cc_final: 0.8290 (tt0) REVERT: D 215 LYS cc_start: 0.9236 (tttt) cc_final: 0.8709 (ttmm) REVERT: D 243 ASN cc_start: 0.8484 (t0) cc_final: 0.7974 (t0) REVERT: D 274 LYS cc_start: 0.9011 (mttt) cc_final: 0.8670 (mmtt) REVERT: D 426 TRP cc_start: 0.8683 (m100) cc_final: 0.8470 (t-100) REVERT: D 433 PHE cc_start: 0.8967 (t80) cc_final: 0.8747 (t80) REVERT: E 82 ASN cc_start: 0.9149 (m-40) cc_final: 0.8817 (m-40) REVERT: E 118 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8353 (mppt) REVERT: E 179 MET cc_start: 0.8748 (mpp) cc_final: 0.8478 (tpp) REVERT: E 213 GLN cc_start: 0.8844 (tt0) cc_final: 0.8538 (tt0) REVERT: E 224 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6574 (tm-30) REVERT: E 253 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7844 (pp30) REVERT: E 313 TYR cc_start: 0.9421 (t80) cc_final: 0.9056 (t80) REVERT: L 3 GLN cc_start: 0.8544 (mp-120) cc_final: 0.8144 (mp10) REVERT: L 433 GLU cc_start: 0.8769 (pt0) cc_final: 0.8440 (pm20) REVERT: L 464 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8167 (p0) REVERT: L 469 GLU cc_start: 0.8192 (mp0) cc_final: 0.7919 (mp0) REVERT: L 472 ASN cc_start: 0.9279 (t0) cc_final: 0.8901 (t0) REVERT: L 476 GLU cc_start: 0.8580 (mp0) cc_final: 0.8372 (pm20) REVERT: M 467 TYR cc_start: 0.8549 (m-80) cc_final: 0.7926 (m-80) REVERT: M 469 GLU cc_start: 0.8643 (mp0) cc_final: 0.7924 (mp0) REVERT: M 472 ASN cc_start: 0.9087 (t0) cc_final: 0.8585 (t0) outliers start: 26 outliers final: 16 residues processed: 265 average time/residue: 0.6714 time to fit residues: 194.9794 Evaluate side-chains 260 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 440 LEU 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 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 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 11 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 464 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 ASN B 224 GLN C 303 ASN E 77 HIS ** 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 461 ASN ** 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 = 0.3393 r_free = 0.3393 target = 0.081012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060079 restraints weight = 42473.550| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.25 r_work: 0.2758 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 16132 Z= 0.254 Angle : 0.725 11.890 21964 Z= 0.369 Chirality : 0.046 0.216 2510 Planarity : 0.004 0.065 2682 Dihedral : 4.611 21.908 2140 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.74 % Allowed : 18.85 % Favored : 79.41 % 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: 1.18 (0.20), residues: 1863 helix: 1.62 (0.21), residues: 565 sheet: 0.53 (0.23), residues: 503 loop : 0.51 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 307 TYR 0.031 0.002 TYR D 299 PHE 0.016 0.002 PHE B 306 TRP 0.019 0.002 TRP L 440 HIS 0.005 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (16099) covalent geometry : angle 0.71873 / 0.37 (21872) SS BOND : bond 0.00218 / 0.13 ( 7) SS BOND : angle 0.70366 / 0.45 ( 14) hydrogen bonds : bond 0.03836 / 2.51 ( 793) hydrogen bonds : angle 4.62165 / 3.19 ( 2537) link_ALPHA1-3 : bond 0.00234 / 0.12 ( 3) link_ALPHA1-3 : angle 1.57101 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00166 / 0.09 ( 3) link_ALPHA1-6 : angle 1.67085 / 0.82 ( 9) link_BETA1-4 : bond 0.00325 / 0.19 ( 11) link_BETA1-4 : angle 1.78291 / 1.15 ( 33) link_NAG-ASN : bond 0.00179 / 0.09 ( 9) link_NAG-ASN : angle 1.62641 / 1.07 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6205.91 seconds wall clock time: 106 minutes 28.88 seconds (6388.88 seconds total)