Starting phenix.real_space_refine on Fri Sep 11 15:45:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w2y_21534/09_2026/6w2y_21534.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 43 5.16 5 Cl 4 4.86 5 C 6322 2.51 5 N 1620 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9721 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4731 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 635} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 730 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLU:plan': 21, 'ARG:plan': 11, 'ASP:plan': 14, 'GLN:plan1': 10, 'ASN:plan1': 9, 'TYR:plan': 6, 'PHE:plan': 4, 'HIS:plan': 2, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 4734 Classifications: {'peptide': 664} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 636} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 580 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 22, 'ARG:plan': 11, 'ASP:plan': 16, 'GLN:plan1': 11, 'PHE:plan': 4, 'ASN:plan1': 9, 'TYR:plan': 6, 'HIS:plan': 2, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 365 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N L9Q A 906 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q A 906 " occ=0.99 residue: pdb=" N L9Q B 906 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q B 906 " occ=0.99 Time building chain proxies: 2.83, per 1000 atoms: 0.29 Number of scatterers: 9721 At special positions: 0 Unit cell: (116.6, 75.26, 162.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 43 16.00 P 4 15.00 Mg 2 11.99 O 1726 8.00 N 1620 7.00 C 6322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 129 " distance=2.05 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 644 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 901 " - " ASN A 365 " " NAG B 901 " - " ASN B 397 " " NAG C 1 " - " ASN A 323 " " NAG D 1 " - " ASN B 323 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 420.1 milliseconds 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2494 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 51.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.598A pdb=" N ARG A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.621A pdb=" N THR A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 111 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.683A pdb=" N ASN A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 188 removed outlier: 4.901A pdb=" N LYS A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TRP A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.629A pdb=" N LEU A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.822A pdb=" N CYS A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.843A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.814A pdb=" N GLU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 368 removed outlier: 3.850A pdb=" N ALA A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.599A pdb=" N SER A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 498 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 509 through 526 removed outlier: 4.102A pdb=" N LEU A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 574 removed outlier: 3.603A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 550 " --> pdb=" O CYS A 546 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 568 " --> pdb=" O MET A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 615 removed outlier: 3.875A pdb=" N THR A 596 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 674 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.801A pdb=" N ALA A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 736 through 744 removed outlier: 3.801A pdb=" N MET A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 84 Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.764A pdb=" N THR B 109 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 111 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.777A pdb=" N GLU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 176 through 188 removed outlier: 5.015A pdb=" N LYS B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.602A pdb=" N LEU B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.751A pdb=" N CYS B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.908A pdb=" N GLU B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 368 removed outlier: 3.855A pdb=" N ALA B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.622A pdb=" N SER B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 499 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 509 through 526 removed outlier: 4.197A pdb=" N LEU B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 541 through 575 removed outlier: 4.130A pdb=" N LEU B 550 " --> pdb=" O CYS B 546 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 575 " --> pdb=" O VAL B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 615 removed outlier: 3.771A pdb=" N THR B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 674 Processing helix chain 'B' and resid 685 through 709 Proline residue: B 704 - end of helix Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'B' and resid 715 through 744 removed outlier: 4.376A pdb=" N LEU B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) Proline residue: B 738 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 100 removed outlier: 8.795A pdb=" N LYS A 122 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A 54 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 124 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 123 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU A 148 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 147 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 6.914A pdb=" N ILE A 192 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG A 223 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR A 194 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER A 225 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 196 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE A 244 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 276 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP A 273 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR A 308 " --> pdb=" O TRP A 273 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 275 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ILE A 310 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN A 424 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS A 432 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.717A pdb=" N PHE A 401 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 467 removed outlier: 6.195A pdb=" N ILE A 464 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN A 640 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR A 466 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLU A 642 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 100 removed outlier: 8.872A pdb=" N LYS B 122 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR B 54 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE B 124 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE B 123 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LEU B 148 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 125 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 147 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.777A pdb=" N ILE B 192 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS B 191 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N VAL B 246 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA B 193 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU B 248 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 195 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 245 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ILE B 276 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N GLY B 247 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 308 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS B 305 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 425 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR B 420 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR B 435 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 422 " --> pdb=" O ILE B 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 468 removed outlier: 6.109A pdb=" N ILE B 464 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN B 640 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR B 466 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU B 642 " --> pdb=" O THR B 466 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG B 468 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 10.881A pdb=" N CYS B 644 " --> pdb=" O ARG B 468 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1503 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: 1.91 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1533 1.32 - 1.45: 3079 1.45 - 1.59: 5255 1.59 - 1.72: 4 1.72 - 1.86: 74 Bond restraints: 9945 Sorted by residual: bond pdb=" CA SER A 152 " pdb=" CB SER A 152 " ideal model delta sigma weight residual 1.530 1.455 0.075 1.43e-02 4.89e+03 2.74e+01 bond pdb=" C SER A 149 " pdb=" O SER A 149 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.20e-02 6.94e+03 1.67e+01 bond pdb=" CA SER A 153 " pdb=" CB SER A 153 " ideal model delta sigma weight residual 1.528 1.467 0.060 1.82e-02 3.02e+03 1.10e+01 bond pdb=" C TYR A 150 " pdb=" O TYR A 150 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.38e-02 5.25e+03 1.03e+01 bond pdb=" C13 SGG B 907 " pdb="CL1 SGG B 907 " ideal model delta sigma weight residual 1.724 1.785 -0.061 2.00e-02 2.50e+03 9.32e+00 ... (remaining 9940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 13381 2.48 - 4.96: 180 4.96 - 7.44: 18 7.44 - 9.92: 8 9.92 - 12.40: 1 Bond angle restraints: 13588 Sorted by residual: angle pdb=" C GLY A 277 " pdb=" N TRP A 278 " pdb=" CA TRP A 278 " ideal model delta sigma weight residual 120.28 127.51 -7.23 1.44e+00 4.82e-01 2.52e+01 angle pdb=" CA SER A 149 " pdb=" C SER A 149 " pdb=" O SER A 149 " ideal model delta sigma weight residual 120.70 115.80 4.90 1.15e+00 7.56e-01 1.82e+01 angle pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" O4 NAG A 901 " ideal model delta sigma weight residual 107.29 119.69 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CA SER A 152 " pdb=" C SER A 152 " pdb=" O SER A 152 " ideal model delta sigma weight residual 120.43 116.00 4.43 1.09e+00 8.42e-01 1.65e+01 angle pdb=" CA ASP B 281 " pdb=" C ASP B 281 " pdb=" O ASP B 281 " ideal model delta sigma weight residual 121.19 116.98 4.21 1.10e+00 8.26e-01 1.47e+01 ... (remaining 13583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 5438 25.98 - 51.95: 232 51.95 - 77.93: 17 77.93 - 103.91: 8 103.91 - 129.88: 5 Dihedral angle restraints: 5700 sinusoidal: 1847 harmonic: 3853 Sorted by residual: dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 129 " pdb=" CB CYS B 129 " ideal model delta sinusoidal sigma weight residual 93.00 18.54 74.46 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS A 103 " pdb=" SG CYS A 103 " pdb=" SG CYS A 129 " pdb=" CB CYS A 129 " ideal model delta sinusoidal sigma weight residual 93.00 41.91 51.09 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" C21 L9Q B 906 " pdb=" C22 L9Q B 906 " pdb=" C23 L9Q B 906 " pdb=" C24 L9Q B 906 " ideal model delta sinusoidal sigma weight residual 179.52 -50.60 -129.88 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 5697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 1617 0.310 - 0.620: 2 0.620 - 0.930: 0 0.930 - 1.240: 0 1.240 - 1.550: 1 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.98 -1.55 2.00e-01 2.50e+01 6.01e+01 chirality pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" N2 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.49 -1.95 -0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" C2 L9Q B 906 " pdb=" C1 L9Q B 906 " pdb=" C3 L9Q B 906 " pdb=" O2 L9Q B 906 " both_signs ideal model delta sigma weight residual False 2.36 1.97 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1617 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 307 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C THR B 307 " -0.070 2.00e-02 2.50e+03 pdb=" O THR B 307 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 308 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 150 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C TYR A 150 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR A 150 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 151 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 126 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO A 127 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.039 5.00e-02 4.00e+02 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 814 2.73 - 3.28: 10205 3.28 - 3.82: 15764 3.82 - 4.36: 18837 4.36 - 4.90: 32720 Nonbonded interactions: 78340 Sorted by model distance: nonbonded pdb=" O GLY A 277 " pdb="MG MG A 905 " model vdw 2.193 2.170 nonbonded pdb=" OD2 ASP A 355 " pdb=" OG SER A 405 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A 117 " pdb=" OE2 GLU B 114 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR A 113 " pdb=" OG1 THR B 109 " model vdw 2.242 3.040 nonbonded pdb=" O PHE B 249 " pdb=" OH TYR B 279 " model vdw 2.263 3.040 ... (remaining 78335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 49 through 225 or (resid 226 and (name N or name CA or nam \ e C or name O or name CB )) or resid 227 through 250 or (resid 251 through 254 a \ nd (name N or name CA or name C or name O or name CB )) or resid 255 through 280 \ or (resid 281 through 282 and (name N or name CA or name C or name O or name CB \ )) or resid 283 through 306 or (resid 307 through 308 and (name N or name CA or \ name C or name O or name CB )) or resid 309 through 354 or (resid 355 through 3 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 357 through \ 425 or (resid 426 and (name N or name CA or name C or name O or name CB )) or r \ esid 427 through 443 or (resid 444 and (name N or name CA or name C or name O or \ name CB )) or resid 445 through 648 or (resid 649 and (name N or name CA or nam \ e C or name O or name CB )) or resid 650 through 907)) selection = (chain 'B' and (resid 49 through 220 or (resid 221 and (name N or name CA or nam \ e C or name O or name CB )) or resid 222 through 307 or (resid 308 and (name N o \ r name CA or name C or name O or name CB )) or resid 309 through 343 or (resid 3 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 345 through \ 408 or (resid 409 and (name N or name CA or name C or name O or name CB )) or r \ esid 410 through 461 or (resid 462 through 466 and (name N or name CA or name C \ or name O or name CB )) or resid 467 through 477 or (resid 478 and (name N or na \ me CA or name C or name O or name CB )) or resid 479 through 494 or (resid 495 a \ nd (name N or name CA or name C or name O or name CB )) or resid 496 through 544 \ or (resid 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 570 or (resid 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 676 or resid 683 through 907)) } ncs_group { reference = 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=0.99 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: 3.150 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.640 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.007 0.075 9957 Z= 0.312 Angle : 0.788 17.644 13618 Z= 0.401 Chirality : 0.063 1.550 1620 Planarity : 0.005 0.072 1691 Dihedral : 14.633 129.881 3188 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.12 % Allowed : 14.85 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.19), residues: 1307 helix: -1.99 (0.17), residues: 666 sheet: -2.60 (0.31), residues: 210 loop : -3.36 (0.23), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 212 TYR 0.027 0.002 TYR A 150 PHE 0.015 0.001 PHE A 226 TRP 0.028 0.002 TRP A 278 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.31 ( 9945) covalent geometry : angle 0.73480 / 0.39 (13588) SS BOND : bond 0.01210 / 0.62 ( 6) SS BOND : angle 5.31467 / 3.39 ( 12) hydrogen bonds : bond 0.12575 / 7.90 ( 510) hydrogen bonds : angle 6.55851 / 4.67 ( 1503) link_BETA1-4 : bond 0.00151 / 0.08 ( 2) link_BETA1-4 : angle 1.82935 / 1.00 ( 6) link_NAG-ASN : bond 0.00669 / 0.33 ( 4) link_NAG-ASN : angle 7.95611 / 5.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 121 ILE cc_start: 0.8701 (mt) cc_final: 0.8484 (tt) REVERT: B 190 LYS cc_start: 0.8174 (mptt) cc_final: 0.7852 (mmtm) REVERT: B 419 TRP cc_start: 0.7683 (m-10) cc_final: 0.7239 (m100) REVERT: B 481 LEU cc_start: 0.7624 (mp) cc_final: 0.7380 (mp) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.0979 time to fit residues: 22.9741 Evaluate side-chains 114 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 176 HIS A 305 HIS A 348 GLN A 694 ASN B 99 HIS B 305 HIS B 348 GLN B 365 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133599 restraints weight = 12406.217| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.30 r_work: 0.3341 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9957 Z= 0.175 Angle : 0.639 10.016 13618 Z= 0.313 Chirality : 0.044 0.193 1620 Planarity : 0.004 0.043 1691 Dihedral : 9.483 122.393 1471 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.63 % Allowed : 13.89 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.22), residues: 1307 helix: -0.53 (0.19), residues: 689 sheet: -2.03 (0.31), residues: 226 loop : -2.35 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 141 TYR 0.033 0.002 TYR A 113 PHE 0.012 0.002 PHE A 656 TRP 0.010 0.001 TRP A 187 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 9945) covalent geometry : angle 0.62731 / 0.31 (13588) SS BOND : bond 0.00560 / 0.30 ( 6) SS BOND : angle 2.07403 / 1.15 ( 12) hydrogen bonds : bond 0.03737 / 2.49 ( 510) hydrogen bonds : angle 4.73871 / 3.35 ( 1503) link_BETA1-4 : bond 0.00235 / 0.12 ( 2) link_BETA1-4 : angle 1.09153 / 0.63 ( 6) link_NAG-ASN : bond 0.00268 / 0.13 ( 4) link_NAG-ASN : angle 3.54856 / 2.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.364 Fit side-chains REVERT: A 141 ARG cc_start: 0.8118 (ptt90) cc_final: 0.7891 (ptt180) REVERT: A 142 MET cc_start: 0.8810 (mmm) cc_final: 0.8599 (mmm) REVERT: A 262 TYR cc_start: 0.7820 (t80) cc_final: 0.7540 (t80) REVERT: A 286 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7333 (mp) REVERT: A 298 MET cc_start: 0.7788 (mmm) cc_final: 0.7500 (mmt) REVERT: B 76 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7482 (mt-10) REVERT: B 121 ILE cc_start: 0.8699 (mt) cc_final: 0.8330 (tt) REVERT: B 190 LYS cc_start: 0.8544 (mptt) cc_final: 0.8092 (mmtm) REVERT: B 419 TRP cc_start: 0.8122 (m-10) cc_final: 0.7484 (m100) REVERT: B 551 TRP cc_start: 0.7935 (m100) cc_final: 0.7608 (m100) outliers start: 22 outliers final: 9 residues processed: 150 average time/residue: 0.0935 time to fit residues: 20.2112 Evaluate side-chains 120 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 545 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 70 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.168704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133536 restraints weight = 12319.932| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.35 r_work: 0.3334 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9957 Z= 0.138 Angle : 0.562 7.810 13618 Z= 0.276 Chirality : 0.042 0.212 1620 Planarity : 0.004 0.041 1691 Dihedral : 8.624 115.463 1471 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.75 % Allowed : 15.81 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1307 helix: 0.10 (0.20), residues: 688 sheet: -1.63 (0.33), residues: 220 loop : -1.79 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 141 TYR 0.030 0.002 TYR A 113 PHE 0.012 0.001 PHE A 656 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9945) covalent geometry : angle 0.55541 / 0.27 (13588) SS BOND : bond 0.00310 / 0.18 ( 6) SS BOND : angle 1.41430 / 0.78 ( 12) hydrogen bonds : bond 0.03407 / 2.29 ( 510) hydrogen bonds : angle 4.31614 / 3.04 ( 1503) link_BETA1-4 : bond 0.00474 / 0.24 ( 2) link_BETA1-4 : angle 1.20167 / 0.65 ( 6) link_NAG-ASN : bond 0.00268 / 0.14 ( 4) link_NAG-ASN : angle 2.63860 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.340 Fit side-chains REVERT: A 142 MET cc_start: 0.8871 (mmm) cc_final: 0.8645 (mmm) REVERT: A 262 TYR cc_start: 0.7703 (t80) cc_final: 0.7503 (t80) REVERT: A 298 MET cc_start: 0.7754 (mmm) cc_final: 0.7409 (mmt) REVERT: A 419 TRP cc_start: 0.8416 (m-10) cc_final: 0.8192 (m100) REVERT: A 650 ASN cc_start: 0.7675 (m-40) cc_final: 0.6923 (p0) REVERT: B 76 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7505 (mt-10) REVERT: B 190 LYS cc_start: 0.8723 (mptt) cc_final: 0.8202 (mmtp) REVERT: B 419 TRP cc_start: 0.8095 (m-10) cc_final: 0.7520 (m100) REVERT: B 484 LEU cc_start: 0.8936 (mp) cc_final: 0.8647 (mp) REVERT: B 551 TRP cc_start: 0.7981 (m100) cc_final: 0.7706 (m100) outliers start: 23 outliers final: 10 residues processed: 145 average time/residue: 0.0864 time to fit residues: 18.5214 Evaluate side-chains 121 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 0.0060 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128546 restraints weight = 12572.757| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.40 r_work: 0.3275 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9957 Z= 0.210 Angle : 0.614 8.348 13618 Z= 0.304 Chirality : 0.044 0.166 1620 Planarity : 0.004 0.047 1691 Dihedral : 8.492 107.409 1471 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.35 % Allowed : 16.89 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1307 helix: 0.24 (0.20), residues: 685 sheet: -1.55 (0.32), residues: 223 loop : -1.74 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 255 TYR 0.028 0.002 TYR A 113 PHE 0.019 0.002 PHE A 226 TRP 0.010 0.002 TRP B 551 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 ( 9945) covalent geometry : angle 0.60693 / 0.30 (13588) SS BOND : bond 0.00368 / 0.21 ( 6) SS BOND : angle 1.70190 / 0.89 ( 12) hydrogen bonds : bond 0.03695 / 2.48 ( 510) hydrogen bonds : angle 4.35268 / 3.07 ( 1503) link_BETA1-4 : bond 0.00396 / 0.20 ( 2) link_BETA1-4 : angle 1.09575 / 0.58 ( 6) link_NAG-ASN : bond 0.00298 / 0.15 ( 4) link_NAG-ASN : angle 2.74483 / 1.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.384 Fit side-chains REVERT: A 286 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7340 (mp) REVERT: A 650 ASN cc_start: 0.7615 (m-40) cc_final: 0.6869 (p0) REVERT: B 76 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7843 (mt-10) REVERT: B 190 LYS cc_start: 0.8689 (mptt) cc_final: 0.8180 (mmtp) REVERT: B 317 ASN cc_start: 0.8187 (m110) cc_final: 0.7613 (p0) REVERT: B 419 TRP cc_start: 0.8301 (m-10) cc_final: 0.7700 (m100) REVERT: B 484 LEU cc_start: 0.8833 (mp) cc_final: 0.8602 (mp) outliers start: 28 outliers final: 17 residues processed: 149 average time/residue: 0.0844 time to fit residues: 18.8638 Evaluate side-chains 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 78 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130498 restraints weight = 12498.754| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.41 r_work: 0.3303 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9957 Z= 0.150 Angle : 0.573 8.390 13618 Z= 0.281 Chirality : 0.043 0.176 1620 Planarity : 0.004 0.036 1691 Dihedral : 8.306 102.171 1471 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.35 % Allowed : 16.77 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.23), residues: 1307 helix: 0.47 (0.20), residues: 683 sheet: -1.42 (0.32), residues: 221 loop : -1.52 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.025 0.002 TYR A 262 PHE 0.013 0.001 PHE A 258 TRP 0.009 0.001 TRP A 445 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9945) covalent geometry : angle 0.56668 / 0.28 (13588) SS BOND : bond 0.00390 / 0.22 ( 6) SS BOND : angle 1.60501 / 0.88 ( 12) hydrogen bonds : bond 0.03399 / 2.27 ( 510) hydrogen bonds : angle 4.22634 / 3.00 ( 1503) link_BETA1-4 : bond 0.00361 / 0.18 ( 2) link_BETA1-4 : angle 1.19311 / 0.62 ( 6) link_NAG-ASN : bond 0.00306 / 0.15 ( 4) link_NAG-ASN : angle 2.44046 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 286 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 650 ASN cc_start: 0.7578 (m-40) cc_final: 0.6888 (p0) REVERT: B 76 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7777 (mt-10) REVERT: B 190 LYS cc_start: 0.8725 (mptt) cc_final: 0.8251 (mmtp) REVERT: B 317 ASN cc_start: 0.8100 (m110) cc_final: 0.7593 (p0) REVERT: B 419 TRP cc_start: 0.8313 (m-10) cc_final: 0.7720 (m100) REVERT: B 484 LEU cc_start: 0.8881 (mp) cc_final: 0.8618 (mp) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 0.0836 time to fit residues: 18.3817 Evaluate side-chains 135 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129463 restraints weight = 12525.811| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.43 r_work: 0.3292 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9957 Z= 0.161 Angle : 0.571 10.041 13618 Z= 0.280 Chirality : 0.043 0.180 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.171 96.360 1471 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.11 % Allowed : 17.01 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1307 helix: 0.58 (0.20), residues: 687 sheet: -1.34 (0.32), residues: 224 loop : -1.45 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.020 0.002 TYR A 113 PHE 0.013 0.001 PHE A 226 TRP 0.014 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 9945) covalent geometry : angle 0.56574 / 0.28 (13588) SS BOND : bond 0.00359 / 0.20 ( 6) SS BOND : angle 1.26471 / 0.69 ( 12) hydrogen bonds : bond 0.03403 / 2.28 ( 510) hydrogen bonds : angle 4.18820 / 2.97 ( 1503) link_BETA1-4 : bond 0.00385 / 0.20 ( 2) link_BETA1-4 : angle 1.18638 / 0.61 ( 6) link_NAG-ASN : bond 0.00302 / 0.15 ( 4) link_NAG-ASN : angle 2.40710 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7688 (mtp85) cc_final: 0.6710 (mtt90) REVERT: A 286 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 650 ASN cc_start: 0.7640 (m-40) cc_final: 0.6955 (p0) REVERT: A 706 THR cc_start: 0.8510 (m) cc_final: 0.8189 (p) REVERT: B 76 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7811 (mt-10) REVERT: B 190 LYS cc_start: 0.8807 (mptt) cc_final: 0.8353 (mmtp) REVERT: B 317 ASN cc_start: 0.8044 (m110) cc_final: 0.7558 (p0) REVERT: B 419 TRP cc_start: 0.8343 (m-10) cc_final: 0.7727 (m100) REVERT: B 484 LEU cc_start: 0.8917 (mp) cc_final: 0.8590 (mp) REVERT: B 699 CYS cc_start: 0.8453 (m) cc_final: 0.8175 (m) outliers start: 26 outliers final: 20 residues processed: 143 average time/residue: 0.0764 time to fit residues: 16.4394 Evaluate side-chains 137 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130709 restraints weight = 12407.963| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.41 r_work: 0.3305 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9957 Z= 0.128 Angle : 0.556 14.030 13618 Z= 0.268 Chirality : 0.042 0.192 1620 Planarity : 0.004 0.035 1691 Dihedral : 7.986 90.679 1471 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.87 % Allowed : 17.96 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1307 helix: 0.72 (0.20), residues: 687 sheet: -1.26 (0.33), residues: 224 loop : -1.31 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 265 TYR 0.018 0.001 TYR A 113 PHE 0.011 0.001 PHE A 258 TRP 0.017 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9945) covalent geometry : angle 0.55170 / 0.27 (13588) SS BOND : bond 0.00316 / 0.18 ( 6) SS BOND : angle 1.06305 / 0.57 ( 12) hydrogen bonds : bond 0.03232 / 2.15 ( 510) hydrogen bonds : angle 4.10624 / 2.92 ( 1503) link_BETA1-4 : bond 0.00374 / 0.19 ( 2) link_BETA1-4 : angle 1.19516 / 0.62 ( 6) link_NAG-ASN : bond 0.00299 / 0.15 ( 4) link_NAG-ASN : angle 2.19485 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7684 (mtp85) cc_final: 0.6666 (mtt90) REVERT: A 286 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7315 (mp) REVERT: A 650 ASN cc_start: 0.7538 (m-40) cc_final: 0.6785 (p0) REVERT: B 76 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7933 (mt-10) REVERT: B 190 LYS cc_start: 0.8786 (mptt) cc_final: 0.8336 (mmtp) REVERT: B 317 ASN cc_start: 0.8033 (m110) cc_final: 0.7517 (p0) REVERT: B 419 TRP cc_start: 0.8341 (m-10) cc_final: 0.7750 (m100) REVERT: B 484 LEU cc_start: 0.8893 (mp) cc_final: 0.8566 (mp) REVERT: B 551 TRP cc_start: 0.8156 (m100) cc_final: 0.7757 (m100) outliers start: 24 outliers final: 17 residues processed: 137 average time/residue: 0.0846 time to fit residues: 17.3386 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.165264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130547 restraints weight = 12480.274| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.35 r_work: 0.3293 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9957 Z= 0.134 Angle : 0.556 16.133 13618 Z= 0.268 Chirality : 0.042 0.158 1620 Planarity : 0.004 0.035 1691 Dihedral : 7.806 87.285 1471 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.99 % Allowed : 18.56 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1307 helix: 0.80 (0.20), residues: 694 sheet: -1.21 (0.33), residues: 224 loop : -1.18 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.018 0.001 TYR A 113 PHE 0.010 0.001 PHE A 226 TRP 0.018 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 9945) covalent geometry : angle 0.55125 / 0.27 (13588) SS BOND : bond 0.00279 / 0.16 ( 6) SS BOND : angle 1.03575 / 0.55 ( 12) hydrogen bonds : bond 0.03248 / 2.16 ( 510) hydrogen bonds : angle 4.08323 / 2.90 ( 1503) link_BETA1-4 : bond 0.00357 / 0.18 ( 2) link_BETA1-4 : angle 1.17620 / 0.60 ( 6) link_NAG-ASN : bond 0.00299 / 0.15 ( 4) link_NAG-ASN : angle 2.13819 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 650 ASN cc_start: 0.7526 (m-40) cc_final: 0.6791 (p0) REVERT: B 76 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7782 (mt-10) REVERT: B 190 LYS cc_start: 0.8755 (mptt) cc_final: 0.8334 (mmtp) REVERT: B 317 ASN cc_start: 0.7846 (m110) cc_final: 0.7488 (p0) REVERT: B 419 TRP cc_start: 0.8181 (m-10) cc_final: 0.7514 (m100) REVERT: B 484 LEU cc_start: 0.8925 (mp) cc_final: 0.8575 (mp) REVERT: B 722 LEU cc_start: 0.7725 (mm) cc_final: 0.7434 (mm) outliers start: 25 outliers final: 17 residues processed: 136 average time/residue: 0.0796 time to fit residues: 16.5961 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130164 restraints weight = 12397.267| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.32 r_work: 0.3287 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9957 Z= 0.151 Angle : 0.568 15.864 13618 Z= 0.274 Chirality : 0.042 0.157 1620 Planarity : 0.004 0.036 1691 Dihedral : 7.798 87.805 1471 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.99 % Allowed : 19.16 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1307 helix: 0.84 (0.20), residues: 692 sheet: -1.18 (0.33), residues: 224 loop : -1.18 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.020 0.001 TYR A 113 PHE 0.014 0.001 PHE A 258 TRP 0.018 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9945) covalent geometry : angle 0.56315 / 0.27 (13588) SS BOND : bond 0.00307 / 0.17 ( 6) SS BOND : angle 1.01237 / 0.53 ( 12) hydrogen bonds : bond 0.03334 / 2.21 ( 510) hydrogen bonds : angle 4.10274 / 2.91 ( 1503) link_BETA1-4 : bond 0.00356 / 0.18 ( 2) link_BETA1-4 : angle 1.19100 / 0.61 ( 6) link_NAG-ASN : bond 0.00302 / 0.15 ( 4) link_NAG-ASN : angle 2.19316 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 286 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7376 (mp) REVERT: A 650 ASN cc_start: 0.7515 (m-40) cc_final: 0.6774 (p0) REVERT: B 76 GLU cc_start: 0.8627 (mm-30) cc_final: 0.7995 (mt-10) REVERT: B 190 LYS cc_start: 0.8789 (mptt) cc_final: 0.8367 (mmtp) REVERT: B 317 ASN cc_start: 0.8060 (m110) cc_final: 0.7543 (p0) REVERT: B 419 TRP cc_start: 0.8389 (m-10) cc_final: 0.7695 (m100) REVERT: B 484 LEU cc_start: 0.8990 (mp) cc_final: 0.8754 (mp) REVERT: B 551 TRP cc_start: 0.8138 (m100) cc_final: 0.7771 (m100) outliers start: 25 outliers final: 20 residues processed: 136 average time/residue: 0.0712 time to fit residues: 14.8437 Evaluate side-chains 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.0670 chunk 110 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130649 restraints weight = 12327.309| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.36 r_work: 0.3305 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9957 Z= 0.132 Angle : 0.564 15.990 13618 Z= 0.272 Chirality : 0.042 0.157 1620 Planarity : 0.004 0.036 1691 Dihedral : 7.571 84.232 1471 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.63 % Allowed : 19.52 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1307 helix: 0.95 (0.20), residues: 694 sheet: -1.09 (0.33), residues: 224 loop : -1.11 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.017 0.001 TYR A 113 PHE 0.012 0.001 PHE A 258 TRP 0.017 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9945) covalent geometry : angle 0.55989 / 0.27 (13588) SS BOND : bond 0.00273 / 0.16 ( 6) SS BOND : angle 0.98043 / 0.52 ( 12) hydrogen bonds : bond 0.03224 / 2.14 ( 510) hydrogen bonds : angle 4.05705 / 2.88 ( 1503) link_BETA1-4 : bond 0.00354 / 0.18 ( 2) link_BETA1-4 : angle 1.19981 / 0.62 ( 6) link_NAG-ASN : bond 0.00302 / 0.15 ( 4) link_NAG-ASN : angle 2.10089 / 1.42 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 286 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7342 (mp) REVERT: A 650 ASN cc_start: 0.7506 (m-40) cc_final: 0.6773 (p0) REVERT: B 76 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7944 (mt-10) REVERT: B 190 LYS cc_start: 0.8797 (mptt) cc_final: 0.8250 (mmtp) REVERT: B 317 ASN cc_start: 0.8031 (m110) cc_final: 0.7469 (p0) REVERT: B 340 HIS cc_start: 0.8004 (t70) cc_final: 0.7774 (t-170) REVERT: B 419 TRP cc_start: 0.8421 (m-10) cc_final: 0.7705 (m100) REVERT: B 484 LEU cc_start: 0.8960 (mp) cc_final: 0.8722 (mp) REVERT: B 551 TRP cc_start: 0.8129 (m100) cc_final: 0.7731 (m100) REVERT: B 722 LEU cc_start: 0.7936 (mm) cc_final: 0.7708 (mm) outliers start: 22 outliers final: 18 residues processed: 133 average time/residue: 0.0762 time to fit residues: 15.8082 Evaluate side-chains 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129767 restraints weight = 12422.894| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.45 r_work: 0.3288 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9957 Z= 0.148 Angle : 0.574 15.903 13618 Z= 0.277 Chirality : 0.043 0.157 1620 Planarity : 0.004 0.035 1691 Dihedral : 7.312 84.730 1471 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 19.76 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.23), residues: 1307 helix: 0.97 (0.20), residues: 695 sheet: -1.09 (0.33), residues: 223 loop : -1.11 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.020 0.001 TYR A 113 PHE 0.013 0.001 PHE A 258 TRP 0.026 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9945) covalent geometry : angle 0.56945 / 0.28 (13588) SS BOND : bond 0.00311 / 0.18 ( 6) SS BOND : angle 1.04174 / 0.56 ( 12) hydrogen bonds : bond 0.03287 / 2.19 ( 510) hydrogen bonds : angle 4.06474 / 2.89 ( 1503) link_BETA1-4 : bond 0.00318 / 0.16 ( 2) link_BETA1-4 : angle 1.19506 / 0.61 ( 6) link_NAG-ASN : bond 0.00294 / 0.14 ( 4) link_NAG-ASN : angle 2.13075 / 1.43 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2723.14 seconds wall clock time: 47 minutes 14.42 seconds (2834.42 seconds total)