Starting phenix.real_space_refine on Mon Jul 28 07:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w2y_21534/07_2025/6w2y_21534.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w2y_21534/07_2025/6w2y_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_21534/07_2025/6w2y_21534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w2y_21534/07_2025/6w2y_21534.map" model { file = "/net/cci-nas-00/data/ceres_data/6w2y_21534/07_2025/6w2y_21534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w2y_21534/07_2025/6w2y_21534.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 11} 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: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 11} 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 dihedrals: 6 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 dihedrals: 6 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: 11 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: 11 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: 7.48, per 1000 atoms: 0.77 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: 3.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.00 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: 2.90 Time building geometry restraints manager: 3.41 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: 5626 25.98 - 51.95: 244 51.95 - 77.93: 21 77.93 - 103.91: 8 103.91 - 129.88: 7 Dihedral angle restraints: 5906 sinusoidal: 2053 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 5903 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 744 or resid 901 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 744 or resid 901 through 9 \ 07)) } 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: 37.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.070 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 14.891 129.881 3394 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.002 TRP A 278 HIS 0.005 0.001 HIS B 305 PHE 0.015 0.001 PHE A 226 TYR 0.027 0.002 TYR A 150 ARG 0.003 0.001 ARG A 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 4) link_NAG-ASN : angle 7.95611 ( 12) link_BETA1-4 : bond 0.00151 ( 2) link_BETA1-4 : angle 1.82935 ( 6) hydrogen bonds : bond 0.12575 ( 510) hydrogen bonds : angle 6.55851 ( 1503) SS BOND : bond 0.01210 ( 6) SS BOND : angle 5.31467 ( 12) covalent geometry : bond 0.00700 ( 9945) covalent geometry : angle 0.73480 (13588) *********************** 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 : 1.033 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: 0.2145 time to fit residues: 50.1027 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 : 1.065 ------------------------------------------------------------------------------- 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 111 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3966 r_free = 0.3966 target = 0.168346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131712 restraints weight = 12316.501| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.31 r_work: 0.3353 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9957 Z= 0.182 Angle : 0.639 10.309 13618 Z= 0.313 Chirality : 0.044 0.177 1620 Planarity : 0.004 0.044 1691 Dihedral : 10.337 122.911 1677 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.40 % Allowed : 14.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1307 helix: -0.59 (0.19), residues: 689 sheet: -2.04 (0.32), residues: 226 loop : -2.39 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.005 0.001 HIS A 305 PHE 0.011 0.002 PHE A 656 TYR 0.036 0.002 TYR A 113 ARG 0.005 0.001 ARG A 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 4) link_NAG-ASN : angle 3.71937 ( 12) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 1.23556 ( 6) hydrogen bonds : bond 0.03826 ( 510) hydrogen bonds : angle 4.78320 ( 1503) SS BOND : bond 0.00538 ( 6) SS BOND : angle 2.21248 ( 12) covalent geometry : bond 0.00434 ( 9945) covalent geometry : angle 0.62572 (13588) *********************** 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 154 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.681 Fit side-chains REVERT: A 141 ARG cc_start: 0.8315 (ptt90) cc_final: 0.8060 (ptt180) REVERT: A 142 MET cc_start: 0.8958 (mmm) cc_final: 0.8750 (mmm) REVERT: A 262 TYR cc_start: 0.7941 (t80) cc_final: 0.7666 (t80) REVERT: A 286 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7373 (mp) REVERT: A 298 MET cc_start: 0.7876 (mmm) cc_final: 0.7622 (mmt) REVERT: B 76 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7680 (mt-10) REVERT: B 121 ILE cc_start: 0.8796 (mt) cc_final: 0.8400 (tt) REVERT: B 190 LYS cc_start: 0.8609 (mptt) cc_final: 0.8161 (mmtm) REVERT: B 419 TRP cc_start: 0.8302 (m-10) cc_final: 0.7683 (m100) REVERT: B 484 LEU cc_start: 0.8822 (mp) cc_final: 0.8616 (mp) REVERT: B 551 TRP cc_start: 0.8007 (m100) cc_final: 0.7707 (m100) outliers start: 20 outliers final: 8 residues processed: 148 average time/residue: 0.2358 time to fit residues: 50.6820 Evaluate side-chains 120 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3966 r_free = 0.3966 target = 0.167985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132780 restraints weight = 12372.330| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.35 r_work: 0.3325 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9957 Z= 0.143 Angle : 0.564 7.809 13618 Z= 0.277 Chirality : 0.043 0.205 1620 Planarity : 0.004 0.042 1691 Dihedral : 9.391 115.326 1677 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.99 % Allowed : 15.81 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.23), residues: 1307 helix: 0.10 (0.20), residues: 688 sheet: -1.64 (0.33), residues: 220 loop : -1.81 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 187 HIS 0.002 0.001 HIS B 305 PHE 0.013 0.001 PHE A 656 TYR 0.030 0.002 TYR A 113 ARG 0.004 0.001 ARG A 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 4) link_NAG-ASN : angle 2.71998 ( 12) link_BETA1-4 : bond 0.00432 ( 2) link_BETA1-4 : angle 1.39490 ( 6) hydrogen bonds : bond 0.03392 ( 510) hydrogen bonds : angle 4.32430 ( 1503) SS BOND : bond 0.00510 ( 6) SS BOND : angle 1.54764 ( 12) covalent geometry : bond 0.00343 ( 9945) covalent geometry : angle 0.55589 (13588) *********************** 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 150 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.004 Fit side-chains REVERT: A 142 MET cc_start: 0.8902 (mmm) cc_final: 0.8684 (mmm) REVERT: A 262 TYR cc_start: 0.7727 (t80) cc_final: 0.7505 (t80) REVERT: A 298 MET cc_start: 0.7788 (mmm) cc_final: 0.7430 (mmt) REVERT: A 650 ASN cc_start: 0.7628 (m-40) cc_final: 0.6878 (p0) REVERT: B 76 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7529 (mt-10) REVERT: B 190 LYS cc_start: 0.8732 (mptt) cc_final: 0.8262 (mmtp) REVERT: B 419 TRP cc_start: 0.8142 (m-10) cc_final: 0.7568 (m100) REVERT: B 484 LEU cc_start: 0.8804 (mp) cc_final: 0.8533 (mp) REVERT: B 551 TRP cc_start: 0.7998 (m100) cc_final: 0.7735 (m100) REVERT: B 559 LEU cc_start: 0.7426 (mm) cc_final: 0.7199 (mm) outliers start: 25 outliers final: 11 residues processed: 145 average time/residue: 0.1881 time to fit residues: 40.3301 Evaluate side-chains 122 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 261 VAL 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 62 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.167728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132679 restraints weight = 12249.465| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.29 r_work: 0.3340 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9957 Z= 0.129 Angle : 0.536 8.028 13618 Z= 0.264 Chirality : 0.042 0.158 1620 Planarity : 0.004 0.047 1691 Dihedral : 8.886 104.554 1677 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.63 % Allowed : 16.77 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1307 helix: 0.46 (0.20), residues: 686 sheet: -1.39 (0.33), residues: 223 loop : -1.58 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 419 HIS 0.005 0.001 HIS A 340 PHE 0.011 0.001 PHE A 284 TYR 0.022 0.001 TYR A 113 ARG 0.003 0.000 ARG A 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 4) link_NAG-ASN : angle 2.39414 ( 12) link_BETA1-4 : bond 0.00419 ( 2) link_BETA1-4 : angle 1.31330 ( 6) hydrogen bonds : bond 0.03250 ( 510) hydrogen bonds : angle 4.16056 ( 1503) SS BOND : bond 0.00273 ( 6) SS BOND : angle 1.28673 ( 12) covalent geometry : bond 0.00309 ( 9945) covalent geometry : angle 0.53008 (13588) *********************** 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 149 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.088 Fit side-chains REVERT: A 286 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 298 MET cc_start: 0.7913 (mmm) cc_final: 0.7521 (mmt) REVERT: A 357 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8242 (tt) REVERT: A 650 ASN cc_start: 0.7533 (m-40) cc_final: 0.6753 (p0) REVERT: B 76 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7769 (mt-10) REVERT: B 190 LYS cc_start: 0.8703 (mptt) cc_final: 0.8102 (mmtp) REVERT: B 317 ASN cc_start: 0.8075 (m110) cc_final: 0.7555 (p0) REVERT: B 419 TRP cc_start: 0.8292 (m-10) cc_final: 0.7711 (m100) REVERT: B 484 LEU cc_start: 0.8864 (mp) cc_final: 0.8574 (mp) REVERT: B 551 TRP cc_start: 0.8025 (m100) cc_final: 0.7783 (m100) outliers start: 22 outliers final: 13 residues processed: 145 average time/residue: 0.2141 time to fit residues: 45.5077 Evaluate side-chains 124 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 357 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 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR 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 101 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 63 optimal weight: 0.0040 chunk 114 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3955 r_free = 0.3955 target = 0.166781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132667 restraints weight = 12337.211| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.40 r_work: 0.3322 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9957 Z= 0.142 Angle : 0.553 8.901 13618 Z= 0.269 Chirality : 0.042 0.218 1620 Planarity : 0.004 0.039 1691 Dihedral : 8.572 97.119 1677 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.23 % Allowed : 16.65 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1307 helix: 0.57 (0.20), residues: 686 sheet: -1.31 (0.33), residues: 223 loop : -1.39 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.011 0.001 PHE A 226 TYR 0.020 0.002 TYR B 113 ARG 0.003 0.000 ARG B 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 4) link_NAG-ASN : angle 2.35570 ( 12) link_BETA1-4 : bond 0.00513 ( 2) link_BETA1-4 : angle 1.42678 ( 6) hydrogen bonds : bond 0.03264 ( 510) hydrogen bonds : angle 4.13597 ( 1503) SS BOND : bond 0.00289 ( 6) SS BOND : angle 1.29322 ( 12) covalent geometry : bond 0.00340 ( 9945) covalent geometry : angle 0.54655 (13588) *********************** 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 146 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7575 (mtp85) cc_final: 0.6631 (mtt90) REVERT: A 262 TYR cc_start: 0.7464 (t80) cc_final: 0.7242 (t80) REVERT: A 286 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7380 (mp) REVERT: A 298 MET cc_start: 0.7914 (mmm) cc_final: 0.7602 (mmt) REVERT: A 357 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 650 ASN cc_start: 0.7495 (m-40) cc_final: 0.6812 (p0) REVERT: B 76 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7774 (mt-10) REVERT: B 190 LYS cc_start: 0.8714 (mptt) cc_final: 0.8213 (mmtp) REVERT: B 317 ASN cc_start: 0.8085 (m110) cc_final: 0.7571 (p0) REVERT: B 419 TRP cc_start: 0.8322 (m-10) cc_final: 0.7735 (m100) REVERT: B 484 LEU cc_start: 0.8889 (mp) cc_final: 0.8576 (mp) REVERT: B 551 TRP cc_start: 0.8069 (m100) cc_final: 0.7790 (m100) outliers start: 27 outliers final: 17 residues processed: 143 average time/residue: 0.2042 time to fit residues: 44.0704 Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 357 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 545 VAL 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 27 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3949 r_free = 0.3949 target = 0.166189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131809 restraints weight = 12393.448| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.35 r_work: 0.3314 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 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 = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9957 Z= 0.133 Angle : 0.558 9.701 13618 Z= 0.270 Chirality : 0.042 0.225 1620 Planarity : 0.004 0.034 1691 Dihedral : 8.377 91.276 1677 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.99 % Allowed : 17.01 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1307 helix: 0.72 (0.20), residues: 685 sheet: -1.23 (0.33), residues: 223 loop : -1.31 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.010 0.001 PHE A 226 TYR 0.017 0.001 TYR A 113 ARG 0.002 0.000 ARG A 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 4) link_NAG-ASN : angle 2.25165 ( 12) link_BETA1-4 : bond 0.00355 ( 2) link_BETA1-4 : angle 1.37029 ( 6) hydrogen bonds : bond 0.03243 ( 510) hydrogen bonds : angle 4.07202 ( 1503) SS BOND : bond 0.00358 ( 6) SS BOND : angle 1.26882 ( 12) covalent geometry : bond 0.00317 ( 9945) covalent geometry : angle 0.55231 (13588) *********************** 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 145 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8496 (ptt-90) cc_final: 0.8170 (ptt180) REVERT: A 243 ARG cc_start: 0.7708 (mtp85) cc_final: 0.6647 (mtt90) REVERT: A 262 TYR cc_start: 0.7505 (t80) cc_final: 0.7261 (t80) REVERT: A 286 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7340 (mp) REVERT: A 298 MET cc_start: 0.8014 (mmm) cc_final: 0.7671 (mmt) REVERT: A 650 ASN cc_start: 0.7632 (m-40) cc_final: 0.6956 (p0) REVERT: B 76 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7818 (mt-10) REVERT: B 190 LYS cc_start: 0.8806 (mptt) cc_final: 0.8353 (mmtp) REVERT: B 317 ASN cc_start: 0.7998 (m110) cc_final: 0.7533 (p0) REVERT: B 419 TRP cc_start: 0.8337 (m-10) cc_final: 0.7747 (m100) REVERT: B 484 LEU cc_start: 0.8969 (mp) cc_final: 0.8767 (mp) REVERT: B 551 TRP cc_start: 0.8082 (m100) cc_final: 0.7788 (m100) REVERT: B 722 LEU cc_start: 0.7936 (mm) cc_final: 0.7662 (mm) outliers start: 25 outliers final: 14 residues processed: 141 average time/residue: 0.2479 time to fit residues: 52.7563 Evaluate side-chains 127 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 286 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 chunk 68 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3957 r_free = 0.3957 target = 0.166906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132319 restraints weight = 12471.290| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.43 r_work: 0.3321 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3132 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= 0.124 Angle : 0.549 14.187 13618 Z= 0.263 Chirality : 0.042 0.230 1620 Planarity : 0.004 0.034 1691 Dihedral : 8.138 88.734 1677 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.40 % Allowed : 17.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1307 helix: 0.84 (0.20), residues: 687 sheet: -1.16 (0.33), residues: 223 loop : -1.17 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.011 0.001 PHE B 624 TYR 0.014 0.001 TYR A 113 ARG 0.003 0.000 ARG B 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 4) link_NAG-ASN : angle 2.13838 ( 12) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.29937 ( 6) hydrogen bonds : bond 0.03144 ( 510) hydrogen bonds : angle 4.02382 ( 1503) SS BOND : bond 0.00419 ( 6) SS BOND : angle 1.32767 ( 12) covalent geometry : bond 0.00295 ( 9945) covalent geometry : angle 0.54393 (13588) *********************** 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 136 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8486 (ptt-90) cc_final: 0.8173 (ptt180) REVERT: A 243 ARG cc_start: 0.7663 (mtp85) cc_final: 0.6613 (mtt90) REVERT: A 286 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7341 (mp) REVERT: A 298 MET cc_start: 0.8075 (mmm) cc_final: 0.7769 (tpt) REVERT: A 650 ASN cc_start: 0.7500 (m-40) cc_final: 0.6757 (p0) REVERT: A 706 THR cc_start: 0.8503 (m) cc_final: 0.8124 (p) REVERT: B 76 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7808 (mt-10) REVERT: B 190 LYS cc_start: 0.8805 (mptt) cc_final: 0.8248 (mmtp) REVERT: B 317 ASN cc_start: 0.8002 (m110) cc_final: 0.7494 (p0) REVERT: B 419 TRP cc_start: 0.8315 (m-10) cc_final: 0.7716 (m100) REVERT: B 484 LEU cc_start: 0.8972 (mp) cc_final: 0.8772 (mp) REVERT: B 551 TRP cc_start: 0.8122 (m100) cc_final: 0.7819 (m100) outliers start: 20 outliers final: 14 residues processed: 132 average time/residue: 0.2182 time to fit residues: 42.0477 Evaluate side-chains 126 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 286 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 0.0770 chunk 116 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131825 restraints weight = 12561.993| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.51 r_work: 0.3301 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3286 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= 0.135 Angle : 0.551 14.201 13618 Z= 0.266 Chirality : 0.042 0.195 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.958 86.538 1677 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.75 % Allowed : 18.56 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1307 helix: 0.91 (0.20), residues: 694 sheet: -1.07 (0.33), residues: 223 loop : -1.07 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.010 0.001 PHE A 226 TYR 0.017 0.001 TYR A 113 ARG 0.002 0.000 ARG A 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 4) link_NAG-ASN : angle 2.12539 ( 12) link_BETA1-4 : bond 0.00331 ( 2) link_BETA1-4 : angle 1.26896 ( 6) hydrogen bonds : bond 0.03201 ( 510) hydrogen bonds : angle 4.02445 ( 1503) SS BOND : bond 0.00323 ( 6) SS BOND : angle 1.13651 ( 12) covalent geometry : bond 0.00324 ( 9945) covalent geometry : angle 0.54596 (13588) *********************** 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 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.7979 (ptt180) REVERT: A 243 ARG cc_start: 0.7688 (mtp85) cc_final: 0.6631 (mtt90) REVERT: A 286 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7306 (mp) REVERT: A 298 MET cc_start: 0.7981 (mmm) cc_final: 0.7750 (mmt) REVERT: A 650 ASN cc_start: 0.7529 (m-40) cc_final: 0.6815 (p0) REVERT: A 706 THR cc_start: 0.8413 (m) cc_final: 0.8054 (p) REVERT: B 76 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7769 (mt-10) REVERT: B 190 LYS cc_start: 0.8759 (mptt) cc_final: 0.8334 (mmtp) REVERT: B 317 ASN cc_start: 0.7806 (m110) cc_final: 0.7446 (p0) REVERT: B 340 HIS cc_start: 0.8007 (t70) cc_final: 0.7780 (t-170) REVERT: B 419 TRP cc_start: 0.8167 (m-10) cc_final: 0.7560 (m100) REVERT: B 551 TRP cc_start: 0.8102 (m100) cc_final: 0.7753 (m100) REVERT: B 722 LEU cc_start: 0.7794 (mm) cc_final: 0.7471 (mm) outliers start: 23 outliers final: 17 residues processed: 136 average time/residue: 0.2359 time to fit residues: 49.0177 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 : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 286 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 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 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 Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 32 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132803 restraints weight = 12387.150| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.47 r_work: 0.3324 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3378 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= 0.115 Angle : 0.549 16.429 13618 Z= 0.262 Chirality : 0.042 0.250 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.793 87.576 1677 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.51 % Allowed : 19.28 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1307 helix: 1.04 (0.20), residues: 694 sheet: -0.94 (0.33), residues: 223 loop : -0.98 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.013 0.001 PHE A 258 TYR 0.018 0.001 TYR B 561 ARG 0.002 0.000 ARG A 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 4) link_NAG-ASN : angle 1.97416 ( 12) link_BETA1-4 : bond 0.00282 ( 2) link_BETA1-4 : angle 1.24752 ( 6) hydrogen bonds : bond 0.03121 ( 510) hydrogen bonds : angle 3.98673 ( 1503) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.99668 ( 12) covalent geometry : bond 0.00271 ( 9945) covalent geometry : angle 0.54503 (13588) *********************** 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 142 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8507 (ptt-90) cc_final: 0.8208 (ptt180) REVERT: A 243 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7330 (mpt-90) REVERT: A 298 MET cc_start: 0.8136 (mmm) cc_final: 0.7764 (tpp) REVERT: A 650 ASN cc_start: 0.7524 (m-40) cc_final: 0.6788 (p0) REVERT: A 706 THR cc_start: 0.8524 (m) cc_final: 0.8151 (p) REVERT: B 76 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7915 (mt-10) REVERT: B 190 LYS cc_start: 0.8837 (mptt) cc_final: 0.8391 (mmtp) REVERT: B 317 ASN cc_start: 0.8005 (m110) cc_final: 0.7480 (p0) REVERT: B 340 HIS cc_start: 0.7994 (t70) cc_final: 0.7765 (t-170) REVERT: B 419 TRP cc_start: 0.8366 (m-10) cc_final: 0.7751 (m100) REVERT: B 484 LEU cc_start: 0.8853 (mp) cc_final: 0.8613 (mp) REVERT: B 551 TRP cc_start: 0.8096 (m100) cc_final: 0.7772 (m100) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.2682 time to fit residues: 54.4752 Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 249 PHE 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 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 Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.8980 chunk 128 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 115 optimal weight: 0.0370 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131164 restraints weight = 12512.224| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.49 r_work: 0.3302 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- 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 = 0.86 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 = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9957 Z= 0.142 Angle : 0.575 16.105 13618 Z= 0.274 Chirality : 0.043 0.259 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.768 87.871 1677 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.51 % Allowed : 19.52 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1307 helix: 1.08 (0.20), residues: 694 sheet: -0.92 (0.33), residues: 223 loop : -1.01 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.011 0.001 PHE A 226 TYR 0.018 0.001 TYR A 113 ARG 0.002 0.000 ARG A 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 2.04841 ( 12) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 1.27736 ( 6) hydrogen bonds : bond 0.03255 ( 510) hydrogen bonds : angle 4.03009 ( 1503) SS BOND : bond 0.00306 ( 6) SS BOND : angle 1.07833 ( 12) covalent geometry : bond 0.00341 ( 9945) covalent geometry : angle 0.57134 (13588) ********************** 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 138 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8492 (ptt-90) cc_final: 0.8203 (ptt180) REVERT: A 243 ARG cc_start: 0.7597 (mtp85) cc_final: 0.6596 (mtt90) REVERT: A 298 MET cc_start: 0.8190 (mmm) cc_final: 0.7956 (mmt) REVERT: A 650 ASN cc_start: 0.7495 (m-40) cc_final: 0.6809 (p0) REVERT: A 706 THR cc_start: 0.8545 (m) cc_final: 0.8157 (p) REVERT: B 76 GLU cc_start: 0.8620 (mm-30) cc_final: 0.7968 (mt-10) REVERT: B 190 LYS cc_start: 0.8770 (mptt) cc_final: 0.8346 (mmtp) REVERT: B 317 ASN cc_start: 0.7987 (m110) cc_final: 0.7496 (p0) REVERT: B 340 HIS cc_start: 0.8015 (t70) cc_final: 0.7782 (t-170) REVERT: B 419 TRP cc_start: 0.8399 (m-10) cc_final: 0.7687 (m100) REVERT: B 551 TRP cc_start: 0.8140 (m100) cc_final: 0.7766 (m100) REVERT: B 722 LEU cc_start: 0.7906 (mm) cc_final: 0.7661 (mm) outliers start: 21 outliers final: 18 residues processed: 134 average time/residue: 0.1858 time to fit residues: 37.3494 Evaluate side-chains 133 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 249 PHE 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 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 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 Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3926 r_free = 0.3926 target = 0.163755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128904 restraints weight = 12448.460| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.44 r_work: 0.3275 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 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 = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9957 Z= 0.182 Angle : 0.619 16.224 13618 Z= 0.296 Chirality : 0.045 0.254 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.879 85.105 1677 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.40 % Allowed : 19.64 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1307 helix: 0.99 (0.20), residues: 694 sheet: -1.08 (0.33), residues: 225 loop : -1.09 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 419 HIS 0.002 0.001 HIS B 170 PHE 0.015 0.001 PHE A 226 TYR 0.021 0.001 TYR A 113 ARG 0.004 0.000 ARG B 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 4) link_NAG-ASN : angle 2.22415 ( 12) link_BETA1-4 : bond 0.00213 ( 2) link_BETA1-4 : angle 1.26299 ( 6) hydrogen bonds : bond 0.03436 ( 510) hydrogen bonds : angle 4.13684 ( 1503) SS BOND : bond 0.00400 ( 6) SS BOND : angle 1.17875 ( 12) covalent geometry : bond 0.00440 ( 9945) covalent geometry : angle 0.61470 (13588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6590.46 seconds wall clock time: 119 minutes 42.36 seconds (7182.36 seconds total)