Starting phenix.real_space_refine on Sat Jun 14 11:00:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qn9_14071/06_2025/7qn9_14071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qn9_14071/06_2025/7qn9_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_14071/06_2025/7qn9_14071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qn9_14071/06_2025/7qn9_14071.map" model { file = "/net/cci-nas-00/data/ceres_data/7qn9_14071/06_2025/7qn9_14071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qn9_14071/06_2025/7qn9_14071.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15696 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2693 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 315} Chain breaks: 1 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 bond proxies already assigned to first conformer: 2627 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'HSM': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'D10': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N HSM C 501 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM C 501 " occ=0.70 residue: pdb=" N HSM D 502 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM D 502 " occ=0.70 Time building chain proxies: 10.84, per 1000 atoms: 0.69 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: 4.56 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.19 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: 5.50 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4782 1.34 - 1.46: 4108 1.46 - 1.58: 7050 1.58 - 1.69: 0 1.69 - 1.81: 159 Bond restraints: 16099 Sorted by residual: bond pdb=" C1 BMA a 3 " pdb=" C2 BMA a 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 16094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20799 1.28 - 2.55: 808 2.55 - 3.83: 193 3.83 - 5.11: 48 5.11 - 6.39: 24 Bond angle restraints: 21872 Sorted by residual: angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 116.69 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.86e+01 angle pdb=" C HIS B 267 " pdb=" N LEU B 268 " pdb=" CA LEU B 268 " ideal model delta sigma weight residual 120.38 125.22 -4.84 1.37e+00 5.33e-01 1.25e+01 angle pdb=" C HIS D 267 " pdb=" N LEU D 268 " pdb=" CA LEU D 268 " ideal model delta sigma weight residual 120.38 125.20 -4.82 1.37e+00 5.33e-01 1.24e+01 ... (remaining 21867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 9339 21.75 - 43.49: 325 43.49 - 65.24: 35 65.24 - 86.99: 35 86.99 - 108.73: 19 Dihedral angle restraints: 9753 sinusoidal: 4188 harmonic: 5565 Sorted by residual: dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2091 0.058 - 0.116: 374 0.116 - 0.174: 33 0.174 - 0.231: 7 0.231 - 0.289: 5 Chirality restraints: 2510 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.63e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.52e+01 ... (remaining 2507 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.007 2.00e-02 2.50e+03 1.53e-02 4.68e+00 pdb=" CG TYR C 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " -0.007 2.00e-02 2.50e+03 1.53e-02 4.66e+00 pdb=" CG TYR B 157 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 157 " 0.006 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR D 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 157 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR D 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR D 157 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 157 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR D 157 " 0.022 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 417 2.71 - 3.26: 15527 3.26 - 3.81: 26302 3.81 - 4.35: 33906 4.35 - 4.90: 56253 Nonbonded interactions: 132405 Sorted by model distance: nonbonded pdb=" O TRP M 440 " pdb=" NH1 ARG M 459 " model vdw 2.164 3.120 nonbonded pdb=" O TRP L 440 " pdb=" NH1 ARG L 459 " model vdw 2.165 3.120 nonbonded pdb=" OG1 THR E 215 " pdb=" OD1 ASN E 246 " model vdw 2.224 3.040 nonbonded pdb=" O VAL A 290 " pdb=" OG1 THR A 294 " model vdw 2.257 3.040 nonbonded pdb=" O SER A 305 " pdb=" ND1 HIS A 308 " model vdw 2.267 3.120 ... (remaining 132400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'D' and resid 8 through 447) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.400 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16132 Z= 0.142 Angle : 0.639 6.387 21964 Z= 0.335 Chirality : 0.046 0.289 2510 Planarity : 0.005 0.058 2682 Dihedral : 13.258 108.734 6168 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.48 % Allowed : 3.60 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP L 440 HIS 0.004 0.001 HIS D 267 PHE 0.017 0.001 PHE D 306 TYR 0.022 0.004 TYR B 157 ARG 0.014 0.002 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 9) link_NAG-ASN : angle 1.55412 ( 27) link_ALPHA1-6 : bond 0.00141 ( 3) link_ALPHA1-6 : angle 0.54745 ( 9) link_BETA1-4 : bond 0.00225 ( 11) link_BETA1-4 : angle 1.19642 ( 33) link_ALPHA1-3 : bond 0.00121 ( 3) link_ALPHA1-3 : angle 0.71485 ( 9) hydrogen bonds : bond 0.20689 ( 793) hydrogen bonds : angle 7.39515 ( 2537) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.68315 ( 14) covalent geometry : bond 0.00309 (16099) covalent geometry : angle 0.63578 (21872) *********************** 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 : 1.637 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: 1.5933 time to fit residues: 747.6649 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 : 1.730 ------------------------------------------------------------------------------- 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 158 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 149 ASN A 345 ASN B 243 ASN D 90 GLN D 185 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 233 GLN E 240 HIS ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059950 restraints weight = 52945.427| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.74 r_work: 0.2752 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16132 Z= 0.237 Angle : 0.704 13.738 21964 Z= 0.367 Chirality : 0.046 0.176 2510 Planarity : 0.005 0.066 2682 Dihedral : 8.798 76.960 2673 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.48 % Allowed : 13.87 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1863 helix: 1.73 (0.21), residues: 570 sheet: 0.37 (0.23), residues: 488 loop : 0.73 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 315 HIS 0.008 0.002 HIS E 77 PHE 0.033 0.002 PHE B 293 TYR 0.027 0.002 TYR B 299 ARG 0.009 0.001 ARG E 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 9) link_NAG-ASN : angle 1.53644 ( 27) link_ALPHA1-6 : bond 0.00366 ( 3) link_ALPHA1-6 : angle 1.64174 ( 9) link_BETA1-4 : bond 0.00313 ( 11) link_BETA1-4 : angle 2.13947 ( 33) link_ALPHA1-3 : bond 0.00682 ( 3) link_ALPHA1-3 : angle 2.22800 ( 9) hydrogen bonds : bond 0.04624 ( 793) hydrogen bonds : angle 5.08475 ( 2537) SS BOND : bond 0.00196 ( 7) SS BOND : angle 0.64616 ( 14) covalent geometry : bond 0.00536 (16099) covalent geometry : angle 0.69591 (21872) *********************** 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 327 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8733 (mtm) cc_final: 0.8329 (mmm) REVERT: A 92 GLU cc_start: 0.8583 (pt0) cc_final: 0.7969 (pm20) REVERT: A 260 MET cc_start: 0.8715 (tpp) cc_final: 0.8497 (tpp) REVERT: A 321 TRP cc_start: 0.7712 (m-10) cc_final: 0.6864 (m100) REVERT: B 13 LYS cc_start: 0.8771 (tttt) cc_final: 0.8428 (ttpp) REVERT: B 52 GLU cc_start: 0.8900 (mp0) cc_final: 0.8678 (mp0) REVERT: B 70 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8926 (mtpp) REVERT: B 138 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9062 (mtt) REVERT: B 190 GLU cc_start: 0.8919 (tt0) cc_final: 0.8646 (pt0) REVERT: B 215 LYS cc_start: 0.9276 (tttt) cc_final: 0.8951 (ttmm) REVERT: B 243 ASN cc_start: 0.8306 (m110) cc_final: 0.8102 (t160) REVERT: B 306 PHE cc_start: 0.8159 (t80) cc_final: 0.7491 (t80) REVERT: C 9 MET cc_start: 0.8520 (mtp) cc_final: 0.8031 (mtt) REVERT: C 90 GLN cc_start: 0.8990 (mp10) cc_final: 0.8170 (mp10) REVERT: C 278 VAL cc_start: 0.8683 (t) cc_final: 0.8477 (p) REVERT: C 286 MET cc_start: 0.9080 (mmp) cc_final: 0.8604 (mmm) REVERT: C 302 VAL cc_start: 0.9370 (t) cc_final: 0.9143 (t) REVERT: C 440 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9049 (tp) REVERT: D 13 LYS cc_start: 0.9195 (tttt) cc_final: 0.8447 (tmmt) REVERT: D 21 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8045 (mmmm) REVERT: D 147 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7699 (mm-30) REVERT: D 215 LYS cc_start: 0.9143 (tttt) cc_final: 0.8613 (ttmm) REVERT: D 243 ASN cc_start: 0.8409 (t0) cc_final: 0.8031 (t0) REVERT: D 306 PHE cc_start: 0.7863 (t80) cc_final: 0.7136 (t80) REVERT: D 433 PHE cc_start: 0.8975 (t80) cc_final: 0.8766 (t80) REVERT: E 118 LYS cc_start: 0.8830 (mmtm) cc_final: 0.7986 (mppt) REVERT: E 233 GLN cc_start: 0.8159 (tt0) cc_final: 0.7818 (tp40) REVERT: L 3 GLN cc_start: 0.8241 (mp10) cc_final: 0.7490 (mp10) REVERT: L 472 ASN cc_start: 0.8963 (t0) cc_final: 0.8047 (t0) REVERT: L 474 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8152 (mptm) REVERT: M 11 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7466 (tm) REVERT: M 452 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8746 (ttmm) REVERT: M 459 ARG cc_start: 0.8050 (pmt170) cc_final: 0.7841 (pmt-80) REVERT: M 472 ASN cc_start: 0.8893 (t0) cc_final: 0.8260 (t0) REVERT: M 473 LEU cc_start: 0.9398 (mt) cc_final: 0.9074 (mm) REVERT: M 474 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8297 (mmmt) outliers start: 58 outliers final: 14 residues processed: 300 average time/residue: 1.6053 time to fit residues: 525.4721 Evaluate side-chains 246 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 A residue 305 SER Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 138 MET 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 302 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 445 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 303 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059374 restraints weight = 59687.057| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.01 r_work: 0.2730 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 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 = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3116 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= 0.171 Angle : 0.628 10.352 21964 Z= 0.323 Chirality : 0.045 0.203 2510 Planarity : 0.004 0.038 2682 Dihedral : 7.385 71.511 2666 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.88 % Allowed : 14.89 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1863 helix: 1.73 (0.21), residues: 569 sheet: 0.44 (0.23), residues: 497 loop : 0.73 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 315 HIS 0.005 0.001 HIS A 308 PHE 0.019 0.002 PHE B 306 TYR 0.025 0.002 TYR D 299 ARG 0.007 0.001 ARG E 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 9) link_NAG-ASN : angle 1.51544 ( 27) link_ALPHA1-6 : bond 0.00613 ( 3) link_ALPHA1-6 : angle 1.76090 ( 9) link_BETA1-4 : bond 0.00344 ( 11) link_BETA1-4 : angle 1.85986 ( 33) link_ALPHA1-3 : bond 0.00867 ( 3) link_ALPHA1-3 : angle 1.60357 ( 9) hydrogen bonds : bond 0.04114 ( 793) hydrogen bonds : angle 4.71591 ( 2537) SS BOND : bond 0.00265 ( 7) SS BOND : angle 0.37824 ( 14) covalent geometry : bond 0.00383 (16099) covalent geometry : angle 0.62056 (21872) *********************** 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 298 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 2.135 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 50 ARG cc_start: 0.8881 (ptt-90) cc_final: 0.8458 (ptt90) REVERT: A 91 MET cc_start: 0.8768 (mtm) cc_final: 0.8364 (mmm) REVERT: A 92 GLU cc_start: 0.8623 (pt0) cc_final: 0.7989 (pm20) REVERT: A 321 TRP cc_start: 0.7681 (m-10) cc_final: 0.6812 (m100) REVERT: B 9 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7705 (mmt) REVERT: B 13 LYS cc_start: 0.8888 (tttt) cc_final: 0.8518 (ttpp) REVERT: B 18 LYS cc_start: 0.9259 (pttp) cc_final: 0.8935 (pptt) REVERT: B 138 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9076 (mtt) REVERT: B 215 LYS cc_start: 0.9272 (tttt) cc_final: 0.8949 (ttmm) REVERT: B 274 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8563 (tmtp) REVERT: B 306 PHE cc_start: 0.8101 (t80) cc_final: 0.7765 (t80) REVERT: C 9 MET cc_start: 0.8495 (mtp) cc_final: 0.8037 (mtt) REVERT: C 90 GLN cc_start: 0.8977 (mp10) cc_final: 0.8121 (mp10) REVERT: C 141 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8727 (mpp80) REVERT: D 13 LYS cc_start: 0.9149 (tttt) cc_final: 0.8550 (tmmt) REVERT: D 21 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8340 (mmmm) REVERT: D 102 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9106 (mtmt) REVERT: D 147 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7713 (mm-30) REVERT: D 215 LYS cc_start: 0.9174 (tttt) cc_final: 0.8619 (ttmm) REVERT: D 243 ASN cc_start: 0.8476 (t0) cc_final: 0.7964 (t0) REVERT: D 306 PHE cc_start: 0.7736 (t80) cc_final: 0.7483 (t80) REVERT: D 433 PHE cc_start: 0.8979 (t80) cc_final: 0.8751 (t80) REVERT: E 118 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8203 (mppt) REVERT: E 142 LYS cc_start: 0.9263 (mtmt) cc_final: 0.9036 (mtmm) REVERT: E 224 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6371 (tm-30) REVERT: L 3 GLN cc_start: 0.8475 (mp10) cc_final: 0.7673 (mp10) REVERT: L 469 GLU cc_start: 0.8298 (mp0) cc_final: 0.8041 (mp0) REVERT: L 472 ASN cc_start: 0.9011 (t0) cc_final: 0.8510 (t0) REVERT: M 11 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7335 (tm) REVERT: M 421 MET cc_start: 0.9195 (mmm) cc_final: 0.8977 (mmm) REVERT: M 460 ASP cc_start: 0.7686 (p0) cc_final: 0.6888 (p0) REVERT: M 472 ASN cc_start: 0.9002 (t0) cc_final: 0.8484 (t0) REVERT: M 473 LEU cc_start: 0.9434 (mt) cc_final: 0.8928 (mm) REVERT: M 474 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8394 (mmmt) REVERT: M 504 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8543 (pm20) outliers start: 48 outliers final: 14 residues processed: 277 average time/residue: 1.5581 time to fit residues: 471.3669 Evaluate side-chains 255 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 B residue 138 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 102 LYS 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 302 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU 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 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 80 optimal weight: 0.0070 chunk 57 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 243 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 227 ASN E 253 GLN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060662 restraints weight = 67341.505| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 4.22 r_work: 0.2757 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16132 Z= 0.123 Angle : 0.609 10.790 21964 Z= 0.311 Chirality : 0.044 0.222 2510 Planarity : 0.004 0.056 2682 Dihedral : 6.491 63.894 2666 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.10 % Allowed : 15.67 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1863 helix: 1.78 (0.21), residues: 570 sheet: 0.55 (0.23), residues: 503 loop : 0.71 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 315 HIS 0.005 0.001 HIS A 308 PHE 0.022 0.001 PHE C 293 TYR 0.029 0.001 TYR D 220 ARG 0.008 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 9) link_NAG-ASN : angle 1.41029 ( 27) link_ALPHA1-6 : bond 0.00768 ( 3) link_ALPHA1-6 : angle 1.65352 ( 9) link_BETA1-4 : bond 0.00331 ( 11) link_BETA1-4 : angle 1.61972 ( 33) link_ALPHA1-3 : bond 0.00945 ( 3) link_ALPHA1-3 : angle 1.71388 ( 9) hydrogen bonds : bond 0.03611 ( 793) hydrogen bonds : angle 4.47622 ( 2537) SS BOND : bond 0.00150 ( 7) SS BOND : angle 0.32775 ( 14) covalent geometry : bond 0.00273 (16099) covalent geometry : angle 0.60310 (21872) *********************** 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 289 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 2.027 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: 0.8728 (mtm) cc_final: 0.8327 (mmm) REVERT: A 92 GLU cc_start: 0.8616 (pt0) cc_final: 0.7963 (pm20) REVERT: A 246 MET cc_start: 0.8744 (mmm) cc_final: 0.8031 (mmm) REVERT: A 262 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8896 (mt0) REVERT: A 282 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8672 (ptpp) REVERT: A 321 TRP cc_start: 0.7671 (m-10) cc_final: 0.6795 (m100) REVERT: B 13 LYS cc_start: 0.8833 (tttt) cc_final: 0.8440 (ttpp) REVERT: B 18 LYS cc_start: 0.9258 (pttp) cc_final: 0.8992 (pptt) REVERT: B 138 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.9056 (mtt) REVERT: B 215 LYS cc_start: 0.9281 (tttt) cc_final: 0.8956 (ttmm) REVERT: B 278 VAL cc_start: 0.8424 (t) cc_final: 0.8165 (p) REVERT: C 9 MET cc_start: 0.8513 (mtp) cc_final: 0.8118 (ttm) REVERT: C 90 GLN cc_start: 0.8964 (mp10) cc_final: 0.8073 (mp10) REVERT: C 141 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8756 (mpp80) REVERT: C 244 TYR cc_start: 0.8860 (p90) cc_final: 0.8606 (p90) REVERT: C 424 ASP cc_start: 0.9168 (m-30) cc_final: 0.8843 (m-30) REVERT: D 9 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8063 (tpt) REVERT: D 13 LYS cc_start: 0.9112 (tttt) cc_final: 0.8494 (tmmt) REVERT: D 21 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8363 (mmmm) REVERT: D 147 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7794 (mm-30) REVERT: D 215 LYS cc_start: 0.9172 (tttt) cc_final: 0.8648 (ttmm) REVERT: D 243 ASN cc_start: 0.8433 (t0) cc_final: 0.7891 (t0) REVERT: D 269 ARG cc_start: 0.6954 (tmt-80) cc_final: 0.6573 (tmm160) REVERT: D 306 PHE cc_start: 0.7755 (t80) cc_final: 0.7534 (t80) REVERT: D 433 PHE cc_start: 0.8981 (t80) cc_final: 0.8736 (t80) REVERT: E 118 LYS cc_start: 0.8988 (mmtm) cc_final: 0.8249 (mppt) REVERT: E 142 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8985 (mtmm) REVERT: E 179 MET cc_start: 0.8786 (mpp) cc_final: 0.8535 (tpp) REVERT: E 213 GLN cc_start: 0.8734 (tt0) cc_final: 0.8533 (tt0) REVERT: E 224 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6345 (tm-30) REVERT: E 313 TYR cc_start: 0.9363 (t80) cc_final: 0.9071 (t80) REVERT: L 469 GLU cc_start: 0.8199 (mp0) cc_final: 0.7963 (mp0) REVERT: L 472 ASN cc_start: 0.9000 (t0) cc_final: 0.8521 (t0) REVERT: M 11 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7352 (tm) REVERT: M 459 ARG cc_start: 0.8037 (pmt-80) cc_final: 0.7741 (pmt-80) REVERT: M 460 ASP cc_start: 0.7532 (p0) cc_final: 0.6482 (p0) REVERT: M 464 ASN cc_start: 0.8924 (m-40) cc_final: 0.8665 (p0) REVERT: M 467 TYR cc_start: 0.8348 (m-80) cc_final: 0.7761 (m-80) REVERT: M 469 GLU cc_start: 0.8604 (mp0) cc_final: 0.7763 (mp0) REVERT: M 472 ASN cc_start: 0.9021 (t0) cc_final: 0.8488 (t0) REVERT: M 473 LEU cc_start: 0.9411 (mt) cc_final: 0.9166 (mm) REVERT: M 504 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8556 (pm20) outliers start: 35 outliers final: 12 residues processed: 274 average time/residue: 1.9097 time to fit residues: 569.9963 Evaluate side-chains 256 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 282 LYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 9 MET 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 E residue 224 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 504 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3402 r_free = 0.3402 target = 0.082003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059874 restraints weight = 59262.354| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.95 r_work: 0.2745 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16132 Z= 0.166 Angle : 0.621 12.250 21964 Z= 0.316 Chirality : 0.044 0.224 2510 Planarity : 0.003 0.059 2682 Dihedral : 6.247 61.321 2666 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.58 % Allowed : 16.45 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1863 helix: 1.79 (0.21), residues: 569 sheet: 0.61 (0.23), residues: 503 loop : 0.68 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 315 HIS 0.003 0.001 HIS C 267 PHE 0.017 0.001 PHE C 293 TYR 0.027 0.002 TYR B 299 ARG 0.008 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 9) link_NAG-ASN : angle 1.40912 ( 27) link_ALPHA1-6 : bond 0.00705 ( 3) link_ALPHA1-6 : angle 1.67229 ( 9) link_BETA1-4 : bond 0.00297 ( 11) link_BETA1-4 : angle 1.69685 ( 33) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 1.76438 ( 9) hydrogen bonds : bond 0.03615 ( 793) hydrogen bonds : angle 4.43027 ( 2537) SS BOND : bond 0.00102 ( 7) SS BOND : angle 0.50799 ( 14) covalent geometry : bond 0.00376 (16099) covalent geometry : angle 0.61430 (21872) *********************** 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 293 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 2.504 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: 0.8746 (mtm) cc_final: 0.8343 (mmm) REVERT: A 92 GLU cc_start: 0.8570 (pt0) cc_final: 0.7956 (pm20) REVERT: A 262 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8306 (mt0) REVERT: A 282 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8622 (ptpp) REVERT: A 321 TRP cc_start: 0.7685 (m-10) cc_final: 0.6809 (m100) REVERT: B 13 LYS cc_start: 0.8880 (tttt) cc_final: 0.8475 (ttpp) REVERT: B 18 LYS cc_start: 0.9244 (pttp) cc_final: 0.8978 (pptt) REVERT: B 138 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8993 (mtt) REVERT: B 215 LYS cc_start: 0.9296 (tttt) cc_final: 0.8965 (ttmm) REVERT: B 269 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7589 (ttt-90) REVERT: B 274 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8555 (tmtp) REVERT: C 9 MET cc_start: 0.8506 (mtp) cc_final: 0.8110 (ttm) REVERT: C 90 GLN cc_start: 0.8935 (mp10) cc_final: 0.8042 (mp10) REVERT: C 102 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: C 244 TYR cc_start: 0.8881 (p90) cc_final: 0.8616 (p90) REVERT: C 424 ASP cc_start: 0.9156 (m-30) cc_final: 0.8833 (m-30) REVERT: D 13 LYS cc_start: 0.9123 (tttt) cc_final: 0.8505 (tmmt) REVERT: D 21 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8396 (mmmm) REVERT: D 147 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7599 (mm-30) REVERT: D 215 LYS cc_start: 0.9180 (tttt) cc_final: 0.8693 (ttmm) REVERT: D 243 ASN cc_start: 0.8478 (t0) cc_final: 0.7914 (t0) REVERT: D 306 PHE cc_start: 0.7711 (t80) cc_final: 0.7484 (t80) REVERT: D 426 TRP cc_start: 0.8704 (m100) cc_final: 0.8470 (t-100) REVERT: D 433 PHE cc_start: 0.8975 (t80) cc_final: 0.8721 (t80) REVERT: E 118 LYS cc_start: 0.9045 (mmtm) cc_final: 0.8288 (mppt) REVERT: E 142 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8982 (mtmm) REVERT: E 179 MET cc_start: 0.8718 (mpp) cc_final: 0.8404 (tpp) REVERT: E 213 GLN cc_start: 0.8869 (tt0) cc_final: 0.8501 (tt0) REVERT: E 224 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: E 226 MET cc_start: 0.8014 (ppp) cc_final: 0.7751 (ppp) REVERT: E 313 TYR cc_start: 0.9379 (t80) cc_final: 0.9137 (t80) REVERT: L 407 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8298 (mt) REVERT: L 430 LYS cc_start: 0.8909 (mppt) cc_final: 0.8447 (mptt) REVERT: L 469 GLU cc_start: 0.8247 (mp0) cc_final: 0.7966 (mp0) REVERT: L 472 ASN cc_start: 0.9087 (t0) cc_final: 0.8650 (t0) REVERT: L 501 TYR cc_start: 0.8806 (m-10) cc_final: 0.8601 (m-10) REVERT: M 11 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7422 (tm) REVERT: M 459 ARG cc_start: 0.8038 (pmt-80) cc_final: 0.7811 (pmt-80) REVERT: M 460 ASP cc_start: 0.7389 (p0) cc_final: 0.6881 (p0) REVERT: M 464 ASN cc_start: 0.8937 (m110) cc_final: 0.8724 (p0) REVERT: M 469 GLU cc_start: 0.8620 (mp0) cc_final: 0.7774 (mp0) REVERT: M 472 ASN cc_start: 0.9080 (t0) cc_final: 0.8737 (t0) REVERT: M 473 LEU cc_start: 0.9370 (mt) cc_final: 0.8731 (mm) REVERT: M 474 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8308 (mmmt) REVERT: M 504 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8458 (pm20) outliers start: 43 outliers final: 14 residues processed: 277 average time/residue: 1.8796 time to fit residues: 569.1348 Evaluate side-chains 256 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 282 LYS Chi-restraints excluded: chain B residue 138 MET 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 102 LYS 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 224 GLU 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 Chi-restraints excluded: chain M residue 504 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 158 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN C 224 GLN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3436 r_free = 0.3436 target = 0.083542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061366 restraints weight = 64699.862| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.16 r_work: 0.2774 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3704 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= 0.115 Angle : 0.607 12.023 21964 Z= 0.305 Chirality : 0.043 0.234 2510 Planarity : 0.003 0.040 2682 Dihedral : 5.795 54.817 2666 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.82 % Allowed : 16.57 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1863 helix: 1.83 (0.21), residues: 570 sheet: 0.88 (0.24), residues: 489 loop : 0.59 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 440 HIS 0.004 0.001 HIS D 267 PHE 0.025 0.001 PHE C 293 TYR 0.024 0.001 TYR B 299 ARG 0.011 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 9) link_NAG-ASN : angle 1.27400 ( 27) link_ALPHA1-6 : bond 0.00930 ( 3) link_ALPHA1-6 : angle 1.58370 ( 9) link_BETA1-4 : bond 0.00357 ( 11) link_BETA1-4 : angle 1.42551 ( 33) link_ALPHA1-3 : bond 0.01010 ( 3) link_ALPHA1-3 : angle 1.67240 ( 9) hydrogen bonds : bond 0.03403 ( 793) hydrogen bonds : angle 4.30071 ( 2537) SS BOND : bond 0.00111 ( 7) SS BOND : angle 0.39494 ( 14) covalent geometry : bond 0.00253 (16099) covalent geometry : angle 0.60198 (21872) *********************** 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 309 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 2.121 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: 0.8754 (mtm) cc_final: 0.8371 (mmm) REVERT: A 92 GLU cc_start: 0.8612 (pt0) cc_final: 0.7979 (pm20) REVERT: A 175 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8360 (mmm160) REVERT: A 181 MET cc_start: 0.8784 (mtm) cc_final: 0.8528 (pmm) REVERT: A 262 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8118 (mt0) REVERT: A 267 CYS cc_start: 0.9186 (m) cc_final: 0.8928 (m) REVERT: A 282 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8608 (ptpp) REVERT: A 321 TRP cc_start: 0.7657 (m-10) cc_final: 0.6791 (m100) REVERT: B 13 LYS cc_start: 0.8855 (tttt) cc_final: 0.8475 (ttpp) REVERT: B 18 LYS cc_start: 0.9265 (pttp) cc_final: 0.8995 (pptt) REVERT: B 49 MET cc_start: 0.8917 (ttp) cc_final: 0.8170 (tmm) REVERT: B 70 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9022 (mmtm) REVERT: B 138 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8946 (mtt) REVERT: B 147 GLU cc_start: 0.8919 (tt0) cc_final: 0.8658 (tm-30) REVERT: B 190 GLU cc_start: 0.8877 (tt0) cc_final: 0.8232 (pt0) REVERT: B 215 LYS cc_start: 0.9261 (tttt) cc_final: 0.8924 (ttmm) REVERT: B 269 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7612 (ttm-80) REVERT: B 274 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8507 (tmtp) REVERT: B 298 GLU cc_start: 0.9329 (tm-30) cc_final: 0.9098 (tm-30) REVERT: C 9 MET cc_start: 0.8488 (mtp) cc_final: 0.8115 (ttm) REVERT: C 90 GLN cc_start: 0.8915 (mp10) cc_final: 0.8013 (mp10) REVERT: C 141 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8771 (mpp80) REVERT: C 190 GLU cc_start: 0.9061 (tt0) cc_final: 0.8704 (tt0) REVERT: C 244 TYR cc_start: 0.8857 (p90) cc_final: 0.8610 (p90) REVERT: C 297 LEU cc_start: 0.9396 (mp) cc_final: 0.9122 (mp) REVERT: C 424 ASP cc_start: 0.9083 (m-30) cc_final: 0.8750 (m-30) REVERT: D 13 LYS cc_start: 0.9105 (tttt) cc_final: 0.8473 (tmmt) REVERT: D 21 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8434 (mmmm) REVERT: D 147 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 215 LYS cc_start: 0.9175 (tttt) cc_final: 0.8695 (ttmm) REVERT: D 224 GLN cc_start: 0.8933 (pt0) cc_final: 0.8645 (pm20) REVERT: D 243 ASN cc_start: 0.8418 (t0) cc_final: 0.7892 (t0) REVERT: D 306 PHE cc_start: 0.7696 (t80) cc_final: 0.7483 (t80) REVERT: D 433 PHE cc_start: 0.8978 (t80) cc_final: 0.8729 (t80) REVERT: E 118 LYS cc_start: 0.9052 (mmtm) cc_final: 0.8702 (mmtm) REVERT: E 142 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8946 (mtmm) REVERT: E 179 MET cc_start: 0.8707 (mpp) cc_final: 0.8440 (tpp) REVERT: E 213 GLN cc_start: 0.8811 (tt0) cc_final: 0.8494 (tt0) REVERT: E 224 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6404 (tm-30) REVERT: E 313 TYR cc_start: 0.9349 (t80) cc_final: 0.9050 (t80) REVERT: L 3 GLN cc_start: 0.8647 (mp10) cc_final: 0.8233 (mp10) REVERT: L 407 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8202 (mt) REVERT: L 430 LYS cc_start: 0.8898 (mppt) cc_final: 0.8466 (mptt) REVERT: L 433 GLU cc_start: 0.8894 (pt0) cc_final: 0.8666 (pp20) REVERT: L 464 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8071 (p0) REVERT: L 469 GLU cc_start: 0.8179 (mp0) cc_final: 0.7958 (mp0) REVERT: L 472 ASN cc_start: 0.9067 (t0) cc_final: 0.8573 (t0) REVERT: L 476 GLU cc_start: 0.8515 (mp0) cc_final: 0.8213 (pm20) REVERT: M 11 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7483 (tm) REVERT: M 454 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7157 (ttp80) REVERT: M 460 ASP cc_start: 0.7598 (p0) cc_final: 0.7307 (p0) REVERT: M 469 GLU cc_start: 0.8575 (mp0) cc_final: 0.7663 (mp0) REVERT: M 472 ASN cc_start: 0.9095 (t0) cc_final: 0.8419 (t0) REVERT: M 473 LEU cc_start: 0.9289 (mt) cc_final: 0.8982 (mm) REVERT: M 474 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8256 (mmpt) REVERT: M 477 ASP cc_start: 0.8471 (m-30) cc_final: 0.8208 (m-30) outliers start: 47 outliers final: 14 residues processed: 290 average time/residue: 1.9382 time to fit residues: 615.6611 Evaluate side-chains 266 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 138 MET Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 444 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 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 L residue 407 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 464 ASN Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 454 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN C 267 HIS D 267 HIS ** 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 = 0.3417 r_free = 0.3417 target = 0.082573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061164 restraints weight = 47066.348| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.55 r_work: 0.2785 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16132 Z= 0.147 Angle : 0.632 14.608 21964 Z= 0.318 Chirality : 0.044 0.232 2510 Planarity : 0.003 0.060 2682 Dihedral : 5.697 52.890 2666 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.28 % Allowed : 17.83 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1863 helix: 1.81 (0.21), residues: 570 sheet: 0.86 (0.24), residues: 492 loop : 0.56 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 315 HIS 0.005 0.001 HIS A 184 PHE 0.022 0.001 PHE B 306 TYR 0.026 0.001 TYR B 299 ARG 0.012 0.000 ARG E 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 9) link_NAG-ASN : angle 1.34496 ( 27) link_ALPHA1-6 : bond 0.00793 ( 3) link_ALPHA1-6 : angle 1.57912 ( 9) link_BETA1-4 : bond 0.00322 ( 11) link_BETA1-4 : angle 1.54868 ( 33) link_ALPHA1-3 : bond 0.00876 ( 3) link_ALPHA1-3 : angle 1.77349 ( 9) hydrogen bonds : bond 0.03438 ( 793) hydrogen bonds : angle 4.31266 ( 2537) SS BOND : bond 0.00104 ( 7) SS BOND : angle 0.53514 ( 14) covalent geometry : bond 0.00338 (16099) covalent geometry : angle 0.62660 (21872) *********************** 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 291 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 1.749 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: 0.8766 (mtm) cc_final: 0.8300 (mmm) REVERT: A 92 GLU cc_start: 0.8556 (pt0) cc_final: 0.7949 (pm20) REVERT: A 262 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8229 (mt0) REVERT: A 267 CYS cc_start: 0.9135 (m) cc_final: 0.8858 (m) REVERT: A 282 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8602 (ptpp) REVERT: A 321 TRP cc_start: 0.7665 (m-10) cc_final: 0.6753 (m100) REVERT: B 13 LYS cc_start: 0.8899 (tttt) cc_final: 0.8510 (ttpp) REVERT: B 18 LYS cc_start: 0.9270 (pttp) cc_final: 0.8980 (pptt) REVERT: B 49 MET cc_start: 0.8839 (ttp) cc_final: 0.7947 (pp-130) REVERT: B 190 GLU cc_start: 0.8836 (tt0) cc_final: 0.8206 (pt0) REVERT: B 215 LYS cc_start: 0.9275 (tttt) cc_final: 0.8937 (ttmm) REVERT: B 269 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7729 (ttt-90) REVERT: B 274 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8728 (ttmm) REVERT: C 9 MET cc_start: 0.8465 (mtp) cc_final: 0.8104 (ttm) REVERT: C 90 GLN cc_start: 0.8903 (mp10) cc_final: 0.7974 (mp10) REVERT: C 141 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8729 (mpp80) REVERT: C 244 TYR cc_start: 0.8829 (p90) cc_final: 0.8588 (p90) REVERT: C 297 LEU cc_start: 0.9416 (mp) cc_final: 0.9133 (mp) REVERT: C 424 ASP cc_start: 0.9012 (m-30) cc_final: 0.8709 (m-30) REVERT: D 13 LYS cc_start: 0.9132 (tttt) cc_final: 0.8498 (tmmt) REVERT: D 21 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8423 (mmmm) REVERT: D 147 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 215 LYS cc_start: 0.9169 (tttt) cc_final: 0.8588 (ttmm) REVERT: D 243 ASN cc_start: 0.8479 (t0) cc_final: 0.7947 (t0) REVERT: D 433 PHE cc_start: 0.8970 (t80) cc_final: 0.8712 (t80) REVERT: E 82 ASN cc_start: 0.9186 (m-40) cc_final: 0.8870 (m-40) REVERT: E 142 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8935 (mtmm) REVERT: E 179 MET cc_start: 0.8622 (mpp) cc_final: 0.8356 (tpp) REVERT: E 213 GLN cc_start: 0.8825 (tt0) cc_final: 0.8519 (tt0) REVERT: E 224 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: E 313 TYR cc_start: 0.9355 (t80) cc_final: 0.9039 (t80) REVERT: L 407 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8206 (mt) REVERT: L 464 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8333 (p0) REVERT: L 469 GLU cc_start: 0.8189 (mp0) cc_final: 0.7873 (mp0) REVERT: L 472 ASN cc_start: 0.9113 (t0) cc_final: 0.8666 (t0) REVERT: L 476 GLU cc_start: 0.8547 (mp0) cc_final: 0.8335 (pm20) REVERT: M 11 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7580 (tm) REVERT: M 469 GLU cc_start: 0.8572 (mp0) cc_final: 0.7706 (mp0) REVERT: M 472 ASN cc_start: 0.9108 (t0) cc_final: 0.8697 (t0) REVERT: M 473 LEU cc_start: 0.9266 (mt) cc_final: 0.9065 (mm) outliers start: 38 outliers final: 12 residues processed: 275 average time/residue: 1.5497 time to fit residues: 464.9343 Evaluate side-chains 263 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 224 GLU 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 464 ASN 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 37 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN C 267 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.058939 restraints weight = 61726.885| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.04 r_work: 0.2724 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16132 Z= 0.190 Angle : 0.662 9.306 21964 Z= 0.335 Chirality : 0.045 0.235 2510 Planarity : 0.003 0.037 2682 Dihedral : 5.691 51.361 2666 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.46 % Allowed : 17.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1863 helix: 1.80 (0.21), residues: 570 sheet: 0.66 (0.23), residues: 504 loop : 0.61 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 PHE 0.021 0.002 PHE B 306 TYR 0.028 0.002 TYR D 299 ARG 0.004 0.000 ARG E 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 9) link_NAG-ASN : angle 1.46240 ( 27) link_ALPHA1-6 : bond 0.00591 ( 3) link_ALPHA1-6 : angle 1.56554 ( 9) link_BETA1-4 : bond 0.00317 ( 11) link_BETA1-4 : angle 1.65227 ( 33) link_ALPHA1-3 : bond 0.00808 ( 3) link_ALPHA1-3 : angle 1.79861 ( 9) hydrogen bonds : bond 0.03576 ( 793) hydrogen bonds : angle 4.39703 ( 2537) SS BOND : bond 0.00171 ( 7) SS BOND : angle 0.54773 ( 14) covalent geometry : bond 0.00434 (16099) covalent geometry : angle 0.65623 (21872) *********************** 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 301 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 1.877 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: 0.8694 (mtm) cc_final: 0.8323 (mmm) REVERT: A 92 GLU cc_start: 0.8646 (pt0) cc_final: 0.8012 (pm20) REVERT: A 262 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8923 (mt0) REVERT: A 267 CYS cc_start: 0.9192 (m) cc_final: 0.8913 (m) REVERT: A 282 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8626 (ptpp) REVERT: A 321 TRP cc_start: 0.7718 (m-10) cc_final: 0.6791 (m100) REVERT: B 13 LYS cc_start: 0.8913 (tttt) cc_final: 0.8529 (ttpp) REVERT: B 18 LYS cc_start: 0.9275 (pttp) cc_final: 0.8870 (pptt) REVERT: B 49 MET cc_start: 0.8891 (ttp) cc_final: 0.8019 (pp-130) REVERT: B 147 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8520 (tm-30) REVERT: B 190 GLU cc_start: 0.8857 (tt0) cc_final: 0.8172 (pt0) REVERT: B 215 LYS cc_start: 0.9289 (tttt) cc_final: 0.8975 (ttmm) REVERT: C 9 MET cc_start: 0.8411 (mtp) cc_final: 0.8003 (ttm) REVERT: C 84 ASP cc_start: 0.8486 (t70) cc_final: 0.7964 (t70) REVERT: C 90 GLN cc_start: 0.8874 (mp10) cc_final: 0.7937 (mp10) REVERT: C 244 TYR cc_start: 0.8881 (p90) cc_final: 0.8599 (p90) REVERT: C 297 LEU cc_start: 0.9469 (mp) cc_final: 0.9222 (mp) REVERT: C 424 ASP cc_start: 0.9055 (m-30) cc_final: 0.8729 (m-30) REVERT: D 13 LYS cc_start: 0.9119 (tttt) cc_final: 0.8499 (tmmt) REVERT: D 147 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7800 (mm-30) REVERT: D 190 GLU cc_start: 0.8773 (tt0) cc_final: 0.8409 (tt0) REVERT: D 215 LYS cc_start: 0.9190 (tttt) cc_final: 0.8617 (ttmm) REVERT: D 243 ASN cc_start: 0.8516 (t0) cc_final: 0.8001 (t0) REVERT: D 274 LYS cc_start: 0.8992 (mttt) cc_final: 0.8665 (mmtt) REVERT: D 426 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7870 (m-90) REVERT: D 433 PHE cc_start: 0.8992 (t80) cc_final: 0.8754 (t80) REVERT: E 82 ASN cc_start: 0.9043 (m-40) cc_final: 0.8696 (m-40) REVERT: E 118 LYS cc_start: 0.9073 (mmtm) cc_final: 0.8493 (mptp) REVERT: E 142 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8973 (mtmm) REVERT: E 179 MET cc_start: 0.8703 (mpp) cc_final: 0.8413 (tpp) REVERT: E 213 GLN cc_start: 0.8862 (tt0) cc_final: 0.8540 (tt0) REVERT: E 226 MET cc_start: 0.7859 (ppp) cc_final: 0.7458 (pmm) REVERT: E 228 PHE cc_start: 0.8613 (m-80) cc_final: 0.8300 (m-80) REVERT: E 313 TYR cc_start: 0.9377 (t80) cc_final: 0.9015 (t80) REVERT: L 464 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8201 (p0) REVERT: L 469 GLU cc_start: 0.8164 (mp0) cc_final: 0.7858 (mp0) REVERT: L 472 ASN cc_start: 0.9247 (t0) cc_final: 0.8857 (t0) REVERT: L 476 GLU cc_start: 0.8568 (mp0) cc_final: 0.8354 (pm20) REVERT: M 11 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7657 (tm) REVERT: M 460 ASP cc_start: 0.7132 (p0) cc_final: 0.6368 (p0) REVERT: M 467 TYR cc_start: 0.8407 (m-80) cc_final: 0.7615 (m-80) REVERT: M 469 GLU cc_start: 0.8626 (mp0) cc_final: 0.7790 (mp0) REVERT: M 472 ASN cc_start: 0.9107 (t0) cc_final: 0.8486 (t0) REVERT: M 473 LEU cc_start: 0.9272 (mt) cc_final: 0.9043 (mm) REVERT: M 474 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7865 (mtpp) outliers start: 41 outliers final: 15 residues processed: 283 average time/residue: 1.4903 time to fit residues: 459.5418 Evaluate side-chains 261 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU 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 474 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.9980 chunk 187 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN D 224 GLN ** 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 = 0.3416 r_free = 0.3416 target = 0.082429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060284 restraints weight = 56093.937| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.83 r_work: 0.2764 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- 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 = 0.31 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 = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16132 Z= 0.149 Angle : 0.670 10.471 21964 Z= 0.337 Chirality : 0.045 0.247 2510 Planarity : 0.004 0.071 2682 Dihedral : 5.489 48.217 2666 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.98 % Allowed : 18.67 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1863 helix: 1.75 (0.21), residues: 570 sheet: 0.61 (0.23), residues: 504 loop : 0.59 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 315 HIS 0.003 0.001 HIS A 308 PHE 0.022 0.001 PHE D 306 TYR 0.027 0.002 TYR B 299 ARG 0.016 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 9) link_NAG-ASN : angle 1.38438 ( 27) link_ALPHA1-6 : bond 0.00839 ( 3) link_ALPHA1-6 : angle 1.52802 ( 9) link_BETA1-4 : bond 0.00325 ( 11) link_BETA1-4 : angle 1.50905 ( 33) link_ALPHA1-3 : bond 0.00864 ( 3) link_ALPHA1-3 : angle 1.66253 ( 9) hydrogen bonds : bond 0.03521 ( 793) hydrogen bonds : angle 4.38112 ( 2537) SS BOND : bond 0.00094 ( 7) SS BOND : angle 0.46384 ( 14) covalent geometry : bond 0.00345 (16099) covalent geometry : angle 0.66561 (21872) *********************** 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 299 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.586 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: 0.8857 (mtm) cc_final: 0.8357 (mmm) REVERT: A 92 GLU cc_start: 0.8621 (pt0) cc_final: 0.8057 (pm20) REVERT: A 160 ILE cc_start: 0.9369 (mt) cc_final: 0.9155 (mp) REVERT: A 267 CYS cc_start: 0.9212 (m) cc_final: 0.8949 (m) REVERT: A 282 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8603 (ptpp) REVERT: A 321 TRP cc_start: 0.7675 (m-10) cc_final: 0.6785 (m100) REVERT: B 13 LYS cc_start: 0.8933 (tttt) cc_final: 0.8539 (ttpp) REVERT: B 18 LYS cc_start: 0.9247 (pttp) cc_final: 0.8888 (pptt) REVERT: B 49 MET cc_start: 0.8805 (ttp) cc_final: 0.8016 (pp-130) REVERT: B 147 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8549 (tm-30) REVERT: B 190 GLU cc_start: 0.8779 (tt0) cc_final: 0.8272 (pt0) REVERT: C 9 MET cc_start: 0.8432 (mtp) cc_final: 0.8005 (ttm) REVERT: C 84 ASP cc_start: 0.8441 (t70) cc_final: 0.7952 (t70) REVERT: C 90 GLN cc_start: 0.8902 (mp10) cc_final: 0.7977 (mp10) REVERT: C 244 TYR cc_start: 0.8883 (p90) cc_final: 0.8635 (p90) REVERT: C 297 LEU cc_start: 0.9501 (mp) cc_final: 0.9272 (mp) REVERT: C 424 ASP cc_start: 0.9005 (m-30) cc_final: 0.8694 (m-30) REVERT: D 13 LYS cc_start: 0.9165 (tttt) cc_final: 0.8541 (tmmt) REVERT: D 21 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8334 (mtmm) REVERT: D 147 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7778 (mm-30) REVERT: D 181 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8140 (mm) REVERT: D 182 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8011 (mm-30) REVERT: D 190 GLU cc_start: 0.8691 (tt0) cc_final: 0.8347 (tt0) REVERT: D 215 LYS cc_start: 0.9162 (tttt) cc_final: 0.8585 (ttmm) REVERT: D 243 ASN cc_start: 0.8484 (t0) cc_final: 0.7972 (t0) REVERT: D 274 LYS cc_start: 0.8991 (mttt) cc_final: 0.8738 (mptt) REVERT: D 433 PHE cc_start: 0.8976 (t80) cc_final: 0.8744 (t80) REVERT: E 82 ASN cc_start: 0.9019 (m-40) cc_final: 0.8706 (m-40) REVERT: E 118 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8632 (mppt) REVERT: E 179 MET cc_start: 0.8672 (mpp) cc_final: 0.8442 (tpp) REVERT: E 213 GLN cc_start: 0.8855 (tt0) cc_final: 0.8551 (tt0) REVERT: E 224 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: E 226 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (ppp) REVERT: E 228 PHE cc_start: 0.8581 (m-80) cc_final: 0.8297 (m-80) REVERT: E 313 TYR cc_start: 0.9400 (t80) cc_final: 0.9020 (t80) REVERT: E 334 ASN cc_start: 0.9023 (m-40) cc_final: 0.8718 (m110) REVERT: L 3 GLN cc_start: 0.8715 (mp10) cc_final: 0.8413 (mp10) REVERT: L 464 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8322 (p0) REVERT: L 469 GLU cc_start: 0.8159 (mp0) cc_final: 0.7853 (mp0) REVERT: L 472 ASN cc_start: 0.9267 (t0) cc_final: 0.8899 (t0) REVERT: M 11 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7601 (tm) REVERT: M 460 ASP cc_start: 0.7141 (p0) cc_final: 0.6896 (p0) REVERT: M 469 GLU cc_start: 0.8628 (mp0) cc_final: 0.7885 (mp0) REVERT: M 472 ASN cc_start: 0.9107 (t0) cc_final: 0.8492 (t0) REVERT: M 473 LEU cc_start: 0.9199 (mt) cc_final: 0.8962 (mm) REVERT: M 474 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8037 (mtpp) outliers start: 33 outliers final: 14 residues processed: 284 average time/residue: 1.3866 time to fit residues: 430.6320 Evaluate side-chains 264 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 464 ASN Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 455 PHE Chi-restraints excluded: chain M residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 128 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 96 optimal weight: 0.0070 chunk 72 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN C 224 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 253 GLN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061165 restraints weight = 69501.744| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.22 r_work: 0.2775 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16132 Z= 0.132 Angle : 0.686 12.271 21964 Z= 0.343 Chirality : 0.045 0.313 2510 Planarity : 0.003 0.066 2682 Dihedral : 5.292 44.965 2666 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.50 % Allowed : 19.51 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1863 helix: 1.72 (0.21), residues: 570 sheet: 0.66 (0.23), residues: 504 loop : 0.55 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 315 HIS 0.003 0.000 HIS D 267 PHE 0.028 0.001 PHE B 293 TYR 0.024 0.001 TYR B 299 ARG 0.014 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 9) link_NAG-ASN : angle 1.29770 ( 27) link_ALPHA1-6 : bond 0.00910 ( 3) link_ALPHA1-6 : angle 1.45380 ( 9) link_BETA1-4 : bond 0.00367 ( 11) link_BETA1-4 : angle 1.41512 ( 33) link_ALPHA1-3 : bond 0.00877 ( 3) link_ALPHA1-3 : angle 1.62585 ( 9) hydrogen bonds : bond 0.03490 ( 793) hydrogen bonds : angle 4.36487 ( 2537) SS BOND : bond 0.00107 ( 7) SS BOND : angle 0.52847 ( 14) covalent geometry : bond 0.00306 (16099) covalent geometry : angle 0.68220 (21872) ********************** 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 269 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8733 (mtm) cc_final: 0.8269 (mmm) REVERT: A 92 GLU cc_start: 0.8654 (pt0) cc_final: 0.8058 (pm20) REVERT: A 160 ILE cc_start: 0.9383 (mt) cc_final: 0.9172 (mp) REVERT: A 175 ARG cc_start: 0.8522 (mmm160) cc_final: 0.8106 (tpt170) REVERT: A 321 TRP cc_start: 0.7688 (m-10) cc_final: 0.6827 (m100) REVERT: B 49 MET cc_start: 0.8798 (ttp) cc_final: 0.8029 (pp-130) REVERT: B 147 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 190 GLU cc_start: 0.8780 (tt0) cc_final: 0.8321 (pt0) REVERT: C 9 MET cc_start: 0.8427 (mtp) cc_final: 0.7992 (ttm) REVERT: C 84 ASP cc_start: 0.8454 (t70) cc_final: 0.7947 (t70) REVERT: C 90 GLN cc_start: 0.8887 (mp10) cc_final: 0.7957 (mp10) REVERT: C 153 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8839 (mp0) REVERT: C 244 TYR cc_start: 0.8904 (p90) cc_final: 0.8647 (p90) REVERT: C 297 LEU cc_start: 0.9493 (mp) cc_final: 0.9265 (mp) REVERT: C 424 ASP cc_start: 0.8955 (m-30) cc_final: 0.8605 (m-30) REVERT: D 13 LYS cc_start: 0.9139 (tttt) cc_final: 0.8516 (tmmt) REVERT: D 147 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7712 (mm-30) REVERT: D 190 GLU cc_start: 0.8675 (tt0) cc_final: 0.8413 (tt0) REVERT: D 215 LYS cc_start: 0.9168 (tttt) cc_final: 0.8660 (ttmm) REVERT: D 243 ASN cc_start: 0.8473 (t0) cc_final: 0.7959 (t0) REVERT: D 274 LYS cc_start: 0.8993 (mttt) cc_final: 0.8721 (mmtt) REVERT: D 433 PHE cc_start: 0.8960 (t80) cc_final: 0.8733 (t80) REVERT: E 82 ASN cc_start: 0.8919 (m-40) cc_final: 0.8534 (t0) REVERT: E 118 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8518 (mppt) REVERT: E 179 MET cc_start: 0.8695 (mpp) cc_final: 0.8454 (tpp) REVERT: E 213 GLN cc_start: 0.8866 (tt0) cc_final: 0.8562 (tt0) REVERT: E 224 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: E 313 TYR cc_start: 0.9396 (t80) cc_final: 0.8905 (t80) REVERT: E 334 ASN cc_start: 0.9043 (m-40) cc_final: 0.8744 (m110) REVERT: L 3 GLN cc_start: 0.8684 (mp10) cc_final: 0.8416 (mp10) REVERT: L 464 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8309 (p0) REVERT: L 469 GLU cc_start: 0.8156 (mp0) cc_final: 0.7819 (mp0) REVERT: L 472 ASN cc_start: 0.9296 (t0) cc_final: 0.8968 (t0) REVERT: M 455 PHE cc_start: 0.7470 (m-80) cc_final: 0.6864 (m-10) REVERT: M 469 GLU cc_start: 0.8735 (mp0) cc_final: 0.8006 (mp0) REVERT: M 472 ASN cc_start: 0.9108 (t0) cc_final: 0.8498 (t0) REVERT: M 474 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8046 (mtpp) outliers start: 25 outliers final: 12 residues processed: 260 average time/residue: 1.3785 time to fit residues: 393.7131 Evaluate side-chains 250 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 277 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 464 ASN Chi-restraints excluded: chain M residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 147 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060665 restraints weight = 69015.400| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.14 r_work: 0.2755 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16132 Z= 0.156 Angle : 0.699 17.508 21964 Z= 0.349 Chirality : 0.046 0.351 2510 Planarity : 0.004 0.067 2682 Dihedral : 5.281 43.722 2666 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.20 % Allowed : 20.11 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1863 helix: 1.79 (0.21), residues: 561 sheet: 0.62 (0.23), residues: 505 loop : 0.52 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 315 HIS 0.002 0.001 HIS A 184 PHE 0.039 0.002 PHE B 293 TYR 0.026 0.002 TYR B 299 ARG 0.015 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 9) link_NAG-ASN : angle 1.38722 ( 27) link_ALPHA1-6 : bond 0.00832 ( 3) link_ALPHA1-6 : angle 1.47227 ( 9) link_BETA1-4 : bond 0.00330 ( 11) link_BETA1-4 : angle 1.48890 ( 33) link_ALPHA1-3 : bond 0.00826 ( 3) link_ALPHA1-3 : angle 1.68350 ( 9) hydrogen bonds : bond 0.03543 ( 793) hydrogen bonds : angle 4.41375 ( 2537) SS BOND : bond 0.00060 ( 7) SS BOND : angle 0.50999 ( 14) covalent geometry : bond 0.00362 (16099) covalent geometry : angle 0.69520 (21872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14629.86 seconds wall clock time: 258 minutes 34.84 seconds (15514.84 seconds total)