Starting phenix.real_space_refine on Fri Feb 14 11:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w2y_21534/02_2025/6w2y_21534.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w2y_21534/02_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_21534/02_2025/6w2y_21534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w2y_21534/02_2025/6w2y_21534.map" model { file = "/net/cci-nas-00/data/ceres_data/6w2y_21534/02_2025/6w2y_21534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w2y_21534/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.92, per 1000 atoms: 0.71 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: 2.61 Conformation dependent library (CDL) restraints added in 1.5 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: 1.11 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: 3.46 Time building geometry restraints manager: 3.00 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.590 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- 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 9945 Z= 0.461 Angle : 0.735 12.396 13588 Z= 0.386 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 *********************** 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 : 1.077 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: 0.2245 time to fit residues: 52.0971 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 : 1.145 ------------------------------------------------------------------------------- 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 = 0.168347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131717 restraints weight = 12316.643| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.31 r_work: 0.3354 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 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 = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 9945 Z= 0.285 Angle : 0.626 9.655 13588 Z= 0.309 Chirality : 0.044 0.177 1620 Planarity : 0.004 0.044 1691 Dihedral : 10.337 122.912 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 *********************** 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 : 1.013 Fit side-chains REVERT: A 141 ARG cc_start: 0.8312 (ptt90) cc_final: 0.8058 (ptt180) REVERT: A 142 MET cc_start: 0.8960 (mmm) cc_final: 0.8754 (mmm) REVERT: A 262 TYR cc_start: 0.7932 (t80) cc_final: 0.7659 (t80) REVERT: A 286 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7374 (mp) REVERT: A 298 MET cc_start: 0.7877 (mmm) cc_final: 0.7621 (mmt) REVERT: B 76 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7678 (mt-10) REVERT: B 121 ILE cc_start: 0.8801 (mt) cc_final: 0.8407 (tt) REVERT: B 190 LYS cc_start: 0.8604 (mptt) cc_final: 0.8152 (mmtm) REVERT: B 419 TRP cc_start: 0.8294 (m-10) cc_final: 0.7676 (m100) REVERT: B 484 LEU cc_start: 0.8818 (mp) cc_final: 0.8611 (mp) REVERT: B 551 TRP cc_start: 0.8000 (m100) cc_final: 0.7694 (m100) outliers start: 20 outliers final: 8 residues processed: 148 average time/residue: 0.2192 time to fit residues: 46.2113 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 : 0.991 ------------------------------------------------------------------------------- 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: 0.5980 chunk 86 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.167171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131831 restraints weight = 12385.264| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.35 r_work: 0.3312 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.004 0.049 9945 Z= 0.244 Angle : 0.563 7.823 13588 Z= 0.279 Chirality : 0.043 0.198 1620 Planarity : 0.004 0.043 1691 Dihedral : 9.443 115.580 1677 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.99 % Allowed : 15.93 % Favored : 81.08 % 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: -1.32 (0.23), residues: 1307 helix: 0.07 (0.20), residues: 687 sheet: -1.67 (0.33), residues: 220 loop : -1.86 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.003 0.001 HIS B 305 PHE 0.014 0.001 PHE A 656 TYR 0.030 0.002 TYR A 113 ARG 0.003 0.000 ARG B 255 *********************** 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 148 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.071 Fit side-chains REVERT: A 142 MET cc_start: 0.8895 (mmm) cc_final: 0.8674 (mmm) REVERT: A 262 TYR cc_start: 0.7757 (t80) cc_final: 0.7533 (t80) REVERT: A 298 MET cc_start: 0.7791 (mmm) cc_final: 0.7424 (mmt) REVERT: A 340 HIS cc_start: 0.7277 (m170) cc_final: 0.7064 (t-170) REVERT: A 419 TRP cc_start: 0.8414 (m-10) cc_final: 0.8211 (m100) REVERT: A 650 ASN cc_start: 0.7671 (m-40) cc_final: 0.6924 (p0) REVERT: B 76 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7527 (mt-10) REVERT: B 190 LYS cc_start: 0.8727 (mptt) cc_final: 0.8294 (mmtp) REVERT: B 317 ASN cc_start: 0.7981 (m110) cc_final: 0.7514 (p0) REVERT: B 419 TRP cc_start: 0.8106 (m-10) cc_final: 0.7515 (m100) REVERT: B 484 LEU cc_start: 0.8795 (mp) cc_final: 0.8523 (mp) REVERT: B 551 TRP cc_start: 0.7994 (m100) cc_final: 0.7668 (m100) outliers start: 25 outliers final: 12 residues processed: 144 average time/residue: 0.1921 time to fit residues: 40.8274 Evaluate side-chains 121 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 545 VAL 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: 0.8980 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.164605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130289 restraints weight = 12362.420| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.40 r_work: 0.3297 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 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 = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9945 Z= 0.277 Angle : 0.572 8.177 13588 Z= 0.284 Chirality : 0.043 0.162 1620 Planarity : 0.004 0.046 1691 Dihedral : 8.964 104.626 1677 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.23 % Allowed : 16.41 % Favored : 80.36 % 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: -0.96 (0.23), residues: 1307 helix: 0.33 (0.20), residues: 685 sheet: -1.48 (0.32), residues: 223 loop : -1.65 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 551 HIS 0.003 0.001 HIS B 305 PHE 0.016 0.001 PHE A 226 TYR 0.023 0.002 TYR A 113 ARG 0.003 0.001 ARG B 265 *********************** 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 150 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.089 Fit side-chains REVERT: A 142 MET cc_start: 0.9124 (mmm) cc_final: 0.8911 (mmm) REVERT: A 286 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7308 (mp) REVERT: A 298 MET cc_start: 0.7922 (mmm) cc_final: 0.7554 (mmt) REVERT: A 340 HIS cc_start: 0.7565 (m170) cc_final: 0.7233 (t-170) REVERT: A 357 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 650 ASN cc_start: 0.7566 (m-40) cc_final: 0.6802 (p0) REVERT: B 76 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7813 (mt-10) REVERT: B 190 LYS cc_start: 0.8691 (mptt) cc_final: 0.8183 (mmtp) REVERT: B 317 ASN cc_start: 0.8190 (m110) cc_final: 0.7593 (p0) REVERT: B 419 TRP cc_start: 0.8297 (m-10) cc_final: 0.7703 (m100) REVERT: B 484 LEU cc_start: 0.8895 (mp) cc_final: 0.8581 (mp) REVERT: B 551 TRP cc_start: 0.8092 (m100) cc_final: 0.7739 (m100) outliers start: 27 outliers final: 16 residues processed: 146 average time/residue: 0.1886 time to fit residues: 40.5336 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 : 1.023 ------------------------------------------------------------------------------- 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 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.164647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130205 restraints weight = 12426.126| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.37 r_work: 0.3298 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9945 Z= 0.245 Angle : 0.564 9.296 13588 Z= 0.276 Chirality : 0.043 0.213 1620 Planarity : 0.004 0.038 1691 Dihedral : 8.722 98.521 1677 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.47 % Allowed : 16.77 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.23), residues: 1307 helix: 0.52 (0.20), residues: 683 sheet: -1.37 (0.32), residues: 223 loop : -1.51 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.012 0.001 PHE A 226 TYR 0.019 0.002 TYR A 113 ARG 0.004 0.000 ARG B 265 *********************** 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 150 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.9106 (mmm) cc_final: 0.8899 (mmm) REVERT: A 243 ARG cc_start: 0.7601 (mtp85) cc_final: 0.6663 (mtt90) REVERT: A 262 TYR cc_start: 0.7615 (t80) cc_final: 0.7385 (t80) REVERT: A 286 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 298 MET cc_start: 0.7973 (mmm) cc_final: 0.7589 (mmt) REVERT: A 340 HIS cc_start: 0.7574 (m170) cc_final: 0.7260 (t-90) REVERT: A 650 ASN cc_start: 0.7565 (m-40) cc_final: 0.6884 (p0) REVERT: B 76 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7808 (mt-10) REVERT: B 190 LYS cc_start: 0.8758 (mptt) cc_final: 0.8289 (mmtp) REVERT: B 317 ASN cc_start: 0.8023 (m110) cc_final: 0.7538 (p0) REVERT: B 419 TRP cc_start: 0.8291 (m-10) cc_final: 0.7705 (m100) REVERT: B 484 LEU cc_start: 0.8962 (mp) cc_final: 0.8756 (mp) REVERT: B 699 CYS cc_start: 0.8440 (m) cc_final: 0.8166 (m) outliers start: 29 outliers final: 17 residues processed: 147 average time/residue: 0.1878 time to fit residues: 41.0852 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 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 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.164710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130684 restraints weight = 12452.660| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.45 r_work: 0.3302 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9945 Z= 0.235 Angle : 0.566 10.961 13588 Z= 0.277 Chirality : 0.043 0.242 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.516 93.863 1677 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.99 % Allowed : 17.25 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.23), residues: 1307 helix: 0.63 (0.20), residues: 686 sheet: -1.30 (0.33), residues: 223 loop : -1.43 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.011 0.001 PHE A 226 TYR 0.019 0.001 TYR A 113 ARG 0.002 0.000 ARG B 265 *********************** 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 147 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7677 (mtp85) cc_final: 0.6629 (mtt90) REVERT: A 286 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 298 MET cc_start: 0.8011 (mmm) cc_final: 0.7640 (mmt) REVERT: A 340 HIS cc_start: 0.7631 (m170) cc_final: 0.7305 (t-90) REVERT: A 650 ASN cc_start: 0.7545 (m-40) cc_final: 0.6798 (p0) REVERT: B 76 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7841 (mt-10) REVERT: B 190 LYS cc_start: 0.8801 (mptt) cc_final: 0.8343 (mmtp) REVERT: B 317 ASN cc_start: 0.8018 (m110) cc_final: 0.7531 (p0) REVERT: B 419 TRP cc_start: 0.8331 (m-10) cc_final: 0.7736 (m100) REVERT: B 551 TRP cc_start: 0.8173 (m100) cc_final: 0.7766 (m100) REVERT: B 699 CYS cc_start: 0.8435 (m) cc_final: 0.8171 (m) outliers start: 25 outliers final: 16 residues processed: 143 average time/residue: 0.1850 time to fit residues: 40.1272 Evaluate side-chains 134 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 169 THR 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 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 68 optimal weight: 0.0670 chunk 122 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.165935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131388 restraints weight = 12484.682| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.39 r_work: 0.3315 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 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 = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9945 Z= 0.189 Angle : 0.545 13.861 13588 Z= 0.265 Chirality : 0.042 0.211 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.214 87.685 1677 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 18.44 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.23), residues: 1307 helix: 0.77 (0.20), residues: 688 sheet: -1.18 (0.33), residues: 224 loop : -1.25 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.009 0.001 PHE A 284 TYR 0.015 0.001 TYR A 113 ARG 0.003 0.000 ARG A 141 *********************** 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 139 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7685 (mtp85) cc_final: 0.6655 (mtt90) REVERT: A 286 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7306 (mp) REVERT: A 340 HIS cc_start: 0.7639 (m170) cc_final: 0.7307 (t70) REVERT: A 650 ASN cc_start: 0.7530 (m-40) cc_final: 0.6801 (p0) REVERT: B 76 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7786 (mt-10) REVERT: B 190 LYS cc_start: 0.8825 (mptt) cc_final: 0.8377 (mmtp) REVERT: B 317 ASN cc_start: 0.7994 (m110) cc_final: 0.7496 (p0) REVERT: B 419 TRP cc_start: 0.8338 (m-10) cc_final: 0.7748 (m100) REVERT: B 722 LEU cc_start: 0.7917 (mm) cc_final: 0.7622 (mm) outliers start: 20 outliers final: 13 residues processed: 134 average time/residue: 0.1853 time to fit residues: 36.9301 Evaluate side-chains 125 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 493 LEU Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 99 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 80 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132651 restraints weight = 12550.461| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.47 r_work: 0.3315 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9945 Z= 0.175 Angle : 0.547 14.649 13588 Z= 0.264 Chirality : 0.042 0.199 1620 Planarity : 0.004 0.034 1691 Dihedral : 8.090 87.129 1677 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.28 % Allowed : 19.16 % Favored : 78.56 % 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: -0.12 (0.23), residues: 1307 helix: 0.93 (0.20), residues: 689 sheet: -1.06 (0.33), residues: 224 loop : -1.14 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.008 0.001 PHE B 258 TYR 0.015 0.001 TYR A 113 ARG 0.003 0.000 ARG A 141 *********************** 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: 19 poor density : 121 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8416 (mptt) cc_final: 0.7818 (mptt) REVERT: A 243 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7359 (mmt180) REVERT: A 286 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 298 MET cc_start: 0.7978 (mmm) cc_final: 0.7777 (mmt) REVERT: A 650 ASN cc_start: 0.7515 (m-40) cc_final: 0.6824 (p0) REVERT: A 706 THR cc_start: 0.8374 (m) cc_final: 0.8016 (p) REVERT: B 76 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7741 (mt-10) REVERT: B 190 LYS cc_start: 0.8799 (mptt) cc_final: 0.8372 (mmtp) REVERT: B 317 ASN cc_start: 0.7797 (m110) cc_final: 0.7441 (p0) REVERT: B 340 HIS cc_start: 0.7989 (t70) cc_final: 0.7780 (t-170) REVERT: B 419 TRP cc_start: 0.8149 (m-10) cc_final: 0.7562 (m100) REVERT: B 551 TRP cc_start: 0.8039 (m100) cc_final: 0.7456 (m100) outliers start: 19 outliers final: 16 residues processed: 137 average time/residue: 0.1813 time to fit residues: 38.0809 Evaluate side-chains 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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 493 LEU Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.164535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129839 restraints weight = 12438.134| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.31 r_work: 0.3291 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 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 = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9945 Z= 0.252 Angle : 0.590 16.326 13588 Z= 0.283 Chirality : 0.043 0.246 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.027 87.337 1677 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.87 % Allowed : 18.68 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.23), residues: 1307 helix: 0.87 (0.20), residues: 693 sheet: -1.05 (0.33), residues: 224 loop : -1.15 (0.30), 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 0.014 0.001 PHE A 226 TYR 0.020 0.001 TYR A 113 ARG 0.003 0.000 ARG A 141 *********************** 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 144 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7309 (mmt180) REVERT: A 286 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7331 (mp) REVERT: A 298 MET cc_start: 0.8229 (mmm) cc_final: 0.7999 (mmt) REVERT: A 650 ASN cc_start: 0.7500 (m-40) cc_final: 0.6843 (p0) REVERT: A 706 THR cc_start: 0.8524 (m) cc_final: 0.8157 (p) REVERT: B 76 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7979 (mt-10) REVERT: B 190 LYS cc_start: 0.8784 (mptt) cc_final: 0.8340 (mmtp) REVERT: B 317 ASN cc_start: 0.7996 (m110) cc_final: 0.7520 (p0) REVERT: B 340 HIS cc_start: 0.8021 (t70) cc_final: 0.7794 (t-170) REVERT: B 419 TRP cc_start: 0.8409 (m-10) cc_final: 0.7707 (m100) REVERT: B 551 TRP cc_start: 0.8154 (m100) cc_final: 0.7736 (m100) REVERT: B 561 TYR cc_start: 0.7630 (t80) cc_final: 0.7334 (t80) REVERT: B 722 LEU cc_start: 0.7888 (mm) cc_final: 0.7614 (mm) outliers start: 24 outliers final: 18 residues processed: 139 average time/residue: 0.1764 time to fit residues: 37.1879 Evaluate side-chains 133 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 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 493 LEU Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.164018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128729 restraints weight = 12549.098| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.44 r_work: 0.3281 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9945 Z= 0.269 Angle : 0.616 16.140 13588 Z= 0.294 Chirality : 0.045 0.254 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.962 86.297 1677 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.51 % Allowed : 19.40 % Favored : 78.08 % 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: -0.22 (0.23), residues: 1307 helix: 0.85 (0.20), residues: 695 sheet: -1.14 (0.33), residues: 226 loop : -1.18 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 419 HIS 0.003 0.001 HIS A 305 PHE 0.013 0.001 PHE A 226 TYR 0.021 0.001 TYR A 113 ARG 0.003 0.000 ARG A 141 ********************** 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 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7216 (mpt-90) REVERT: A 286 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7341 (mp) REVERT: A 650 ASN cc_start: 0.7501 (m-40) cc_final: 0.6840 (p0) REVERT: A 706 THR cc_start: 0.8538 (m) cc_final: 0.8167 (p) REVERT: B 76 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7975 (mt-10) REVERT: B 190 LYS cc_start: 0.8782 (mptt) cc_final: 0.8362 (mmtp) REVERT: B 317 ASN cc_start: 0.8036 (m110) cc_final: 0.7534 (p0) REVERT: B 340 HIS cc_start: 0.7962 (t70) cc_final: 0.7723 (t-170) REVERT: B 419 TRP cc_start: 0.8410 (m-10) cc_final: 0.7772 (m100) REVERT: B 551 TRP cc_start: 0.8084 (m100) cc_final: 0.7638 (m100) outliers start: 21 outliers final: 17 residues processed: 136 average time/residue: 0.1839 time to fit residues: 38.0623 Evaluate side-chains 135 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 286 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 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 493 LEU Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 126 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 144 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.161562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126226 restraints weight = 12481.822| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.42 r_work: 0.3248 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9945 Z= 0.344 Angle : 0.676 18.012 13588 Z= 0.320 Chirality : 0.046 0.235 1620 Planarity : 0.004 0.035 1691 Dihedral : 7.925 91.883 1677 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.40 % Allowed : 20.12 % Favored : 77.49 % 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: -0.41 (0.23), residues: 1307 helix: 0.72 (0.20), residues: 694 sheet: -1.23 (0.33), residues: 225 loop : -1.33 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 419 HIS 0.003 0.001 HIS A 305 PHE 0.018 0.002 PHE A 226 TYR 0.026 0.002 TYR A 113 ARG 0.004 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5838.64 seconds wall clock time: 103 minutes 52.61 seconds (6232.61 seconds total)