Starting phenix.real_space_refine on Sun Dec 29 07:56:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w2y_21534/12_2024/6w2y_21534.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w2y_21534/12_2024/6w2y_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_21534/12_2024/6w2y_21534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w2y_21534/12_2024/6w2y_21534.map" model { file = "/net/cci-nas-00/data/ceres_data/6w2y_21534/12_2024/6w2y_21534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w2y_21534/12_2024/6w2y_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9721 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4731 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 635} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 730 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 4734 Classifications: {'peptide': 664} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 636} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 580 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 365 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N L9Q A 906 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q A 906 " occ=0.99 residue: pdb=" N L9Q B 906 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q B 906 " occ=0.99 Time building chain proxies: 7.01, per 1000 atoms: 0.72 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: 2.57 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: 1.05 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: 3.21 Time building geometry restraints manager: 2.93 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: 1.800 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.020 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.750 ------------------------------------------------------------------------------- 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 : 1.073 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: 0.2316 time to fit residues: 53.2672 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 : 1.059 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 1.032 Fit side-chains REVERT: A 77 MET cc_start: 0.8121 (ttm) cc_final: 0.7915 (ttm) REVERT: A 286 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7308 (mp) REVERT: A 298 MET cc_start: 0.7557 (mmm) cc_final: 0.7326 (mmt) REVERT: B 76 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7156 (mt-10) REVERT: B 190 LYS cc_start: 0.8224 (mptt) cc_final: 0.7924 (mmtm) REVERT: B 419 TRP cc_start: 0.7636 (m-10) cc_final: 0.7261 (m100) outliers start: 20 outliers final: 8 residues processed: 148 average time/residue: 0.2050 time to fit residues: 43.5264 Evaluate side-chains 120 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9945 Z= 0.224 Angle : 0.560 7.839 13588 Z= 0.277 Chirality : 0.043 0.198 1620 Planarity : 0.004 0.042 1691 Dihedral : 9.504 116.412 1677 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.75 % Allowed : 16.05 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1307 helix: 0.02 (0.20), residues: 690 sheet: -1.67 (0.33), residues: 220 loop : -1.81 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.003 0.001 HIS B 305 PHE 0.012 0.001 PHE A 656 TYR 0.030 0.002 TYR A 113 ARG 0.011 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.6967 (t80) cc_final: 0.6696 (t80) REVERT: A 298 MET cc_start: 0.7466 (mmm) cc_final: 0.7192 (mmt) REVERT: A 650 ASN cc_start: 0.7473 (m-40) cc_final: 0.6868 (p0) REVERT: B 76 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7219 (mt-10) REVERT: B 419 TRP cc_start: 0.7609 (m-10) cc_final: 0.7247 (m100) REVERT: B 493 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7908 (tt) REVERT: B 559 LEU cc_start: 0.8010 (mm) cc_final: 0.7764 (mm) outliers start: 23 outliers final: 11 residues processed: 146 average time/residue: 0.2077 time to fit residues: 43.9157 Evaluate side-chains 120 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 493 LEU Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9945 Z= 0.361 Angle : 0.629 8.613 13588 Z= 0.313 Chirality : 0.045 0.169 1620 Planarity : 0.004 0.047 1691 Dihedral : 9.204 108.026 1677 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.83 % Allowed : 15.45 % Favored : 80.72 % 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: -1.16 (0.23), residues: 1307 helix: 0.16 (0.20), residues: 686 sheet: -1.57 (0.32), residues: 223 loop : -1.70 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 419 HIS 0.003 0.001 HIS B 170 PHE 0.021 0.002 PHE A 226 TYR 0.029 0.002 TYR A 113 ARG 0.004 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 157 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.068 Fit side-chains REVERT: A 190 LYS cc_start: 0.7808 (mptt) cc_final: 0.7527 (mptt) REVERT: A 286 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7277 (mp) REVERT: A 298 MET cc_start: 0.7690 (mmm) cc_final: 0.7482 (mmt) REVERT: A 650 ASN cc_start: 0.7450 (m-40) cc_final: 0.6821 (p0) REVERT: B 419 TRP cc_start: 0.7628 (m-10) cc_final: 0.7213 (m100) REVERT: B 493 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7957 (tt) REVERT: B 722 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7826 (mm) outliers start: 32 outliers final: 19 residues processed: 153 average time/residue: 0.1775 time to fit residues: 41.1576 Evaluate side-chains 133 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 337 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2964 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= 0.172 Angle : 0.552 12.037 13588 Z= 0.269 Chirality : 0.042 0.181 1620 Planarity : 0.004 0.036 1691 Dihedral : 8.731 98.108 1677 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.99 % Allowed : 16.89 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1307 helix: 0.51 (0.20), residues: 686 sheet: -1.38 (0.33), residues: 220 loop : -1.42 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.012 0.001 PHE A 284 TYR 0.017 0.001 TYR A 113 ARG 0.003 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 146 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 286 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7331 (mp) REVERT: A 650 ASN cc_start: 0.7518 (m-40) cc_final: 0.6956 (p0) REVERT: B 419 TRP cc_start: 0.7616 (m-10) cc_final: 0.7246 (m100) REVERT: B 493 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7907 (tt) REVERT: B 722 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7820 (mm) outliers start: 25 outliers final: 13 residues processed: 142 average time/residue: 0.1908 time to fit residues: 40.3592 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 0.0000 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3111 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= 0.278 Angle : 0.581 9.842 13588 Z= 0.283 Chirality : 0.043 0.165 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.561 94.460 1677 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.75 % Allowed : 17.84 % Favored : 79.40 % 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: -0.63 (0.23), residues: 1307 helix: 0.57 (0.20), residues: 687 sheet: -1.35 (0.32), residues: 224 loop : -1.41 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 419 HIS 0.003 0.001 HIS A 305 PHE 0.015 0.001 PHE A 226 TYR 0.020 0.001 TYR A 113 ARG 0.003 0.000 ARG A 141 *********************** 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 136 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7758 (mtp85) cc_final: 0.6920 (mtt90) REVERT: A 286 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7330 (mp) REVERT: A 650 ASN cc_start: 0.7423 (m-40) cc_final: 0.6910 (p0) REVERT: A 706 THR cc_start: 0.8360 (m) cc_final: 0.8154 (p) REVERT: B 419 TRP cc_start: 0.7612 (m-10) cc_final: 0.7234 (m100) REVERT: B 493 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 699 CYS cc_start: 0.8035 (m) cc_final: 0.7755 (m) REVERT: B 722 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7884 (mm) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.1718 time to fit residues: 35.0192 Evaluate side-chains 132 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 206 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.0370 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9945 Z= 0.202 Angle : 0.553 12.237 13588 Z= 0.268 Chirality : 0.042 0.185 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.352 89.609 1677 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.99 % Allowed : 17.96 % Favored : 79.04 % 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: -0.44 (0.23), residues: 1307 helix: 0.70 (0.20), residues: 687 sheet: -1.26 (0.32), residues: 224 loop : -1.28 (0.30), residues: 396 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 0.010 0.001 PHE A 284 TYR 0.017 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 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7783 (mtp85) cc_final: 0.6868 (mtt90) REVERT: A 286 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 650 ASN cc_start: 0.7428 (m-40) cc_final: 0.6801 (p0) REVERT: A 706 THR cc_start: 0.8386 (m) cc_final: 0.8164 (p) REVERT: B 419 TRP cc_start: 0.7644 (m-10) cc_final: 0.7266 (m100) REVERT: B 493 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7947 (tt) REVERT: B 699 CYS cc_start: 0.8017 (m) cc_final: 0.7802 (m) REVERT: B 722 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7873 (mm) outliers start: 25 outliers final: 17 residues processed: 136 average time/residue: 0.1765 time to fit residues: 36.5833 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3369 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= 0.212 Angle : 0.574 17.403 13588 Z= 0.274 Chirality : 0.042 0.204 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.085 89.381 1677 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.23 % Allowed : 18.20 % 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: -0.27 (0.23), residues: 1307 helix: 0.80 (0.20), residues: 693 sheet: -1.20 (0.33), residues: 224 loop : -1.17 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.011 0.001 PHE A 258 TYR 0.017 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 145 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 286 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 650 ASN cc_start: 0.7444 (m-40) cc_final: 0.6836 (p0) REVERT: A 706 THR cc_start: 0.8418 (m) cc_final: 0.8184 (p) REVERT: B 419 TRP cc_start: 0.7678 (m-10) cc_final: 0.7273 (m100) REVERT: B 493 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7858 (tt) REVERT: B 722 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7885 (mm) outliers start: 27 outliers final: 18 residues processed: 139 average time/residue: 0.1763 time to fit residues: 36.8563 Evaluate side-chains 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain A residue 486 ILE 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 Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 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 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9945 Z= 0.264 Angle : 0.592 16.068 13588 Z= 0.286 Chirality : 0.043 0.218 1620 Planarity : 0.004 0.036 1691 Dihedral : 8.066 87.895 1677 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.75 % Allowed : 19.52 % Favored : 77.72 % 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: -0.28 (0.23), residues: 1307 helix: 0.82 (0.20), residues: 690 sheet: -1.23 (0.32), residues: 224 loop : -1.19 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 419 HIS 0.003 0.001 HIS A 643 PHE 0.017 0.001 PHE A 258 TYR 0.021 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 143 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 650 ASN cc_start: 0.7436 (m-40) cc_final: 0.6834 (p0) REVERT: A 706 THR cc_start: 0.8448 (m) cc_final: 0.8240 (p) REVERT: B 419 TRP cc_start: 0.7718 (m-10) cc_final: 0.7305 (m100) REVERT: B 481 LEU cc_start: 0.8075 (mp) cc_final: 0.7817 (mp) REVERT: B 493 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 722 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7893 (mm) outliers start: 23 outliers final: 20 residues processed: 139 average time/residue: 0.1754 time to fit residues: 37.4682 Evaluate side-chains 135 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 218 ILE 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 Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9945 Z= 0.210 Angle : 0.584 15.584 13588 Z= 0.280 Chirality : 0.043 0.196 1620 Planarity : 0.004 0.036 1691 Dihedral : 7.787 85.433 1677 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.51 % Allowed : 20.12 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1307 helix: 0.94 (0.20), residues: 688 sheet: -1.15 (0.33), residues: 224 loop : -1.07 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.013 0.001 PHE A 258 TYR 0.017 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 137 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 650 ASN cc_start: 0.7429 (m-40) cc_final: 0.6839 (p0) REVERT: A 706 THR cc_start: 0.8446 (m) cc_final: 0.8227 (p) REVERT: B 340 HIS cc_start: 0.7944 (t70) cc_final: 0.7742 (t-170) REVERT: B 419 TRP cc_start: 0.7712 (m-10) cc_final: 0.7286 (m100) REVERT: B 481 LEU cc_start: 0.8121 (mp) cc_final: 0.7864 (mp) REVERT: B 493 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 722 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7842 (mm) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.1734 time to fit residues: 35.6421 Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain A residue 486 ILE 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 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 Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.164605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129399 restraints weight = 12409.860| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.34 r_work: 0.3290 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3617 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= 0.222 Angle : 0.606 18.178 13588 Z= 0.285 Chirality : 0.043 0.200 1620 Planarity : 0.004 0.036 1691 Dihedral : 7.564 84.901 1677 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.28 % Allowed : 19.88 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1307 helix: 0.95 (0.20), residues: 694 sheet: -1.16 (0.33), residues: 225 loop : -1.10 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.013 0.001 PHE A 258 TYR 0.019 0.001 TYR A 113 ARG 0.003 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.37 seconds wall clock time: 40 minutes 27.96 seconds (2427.96 seconds total)