Starting phenix.real_space_refine on Sat Jun 21 02:02:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz9_41738/06_2025/8tz9_41738_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz9_41738/06_2025/8tz9_41738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz9_41738/06_2025/8tz9_41738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz9_41738/06_2025/8tz9_41738.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz9_41738/06_2025/8tz9_41738_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz9_41738/06_2025/8tz9_41738_trim.cif" } resolution = 3.67 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= 0.008 sd= 0.045 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: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 8103 2.51 5 N 1923 2.21 5 O 2115 1.98 5 H 12069 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24297 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.64, per 1000 atoms: 0.48 Number of scatterers: 24297 At special positions: 0 Unit cell: (128.52, 130.68, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 2115 8.00 N 1923 7.00 C 8103 6.00 H 12069 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 2.0 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 90.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 130 through 157 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.683A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.711A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.437A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 removed outlier: 3.534A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.369A pdb=" N THR B 286 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 313 through 330 removed outlier: 3.511A pdb=" N GLY B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.563A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 3.981A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 481 removed outlier: 3.660A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.522A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 496 " --> pdb=" O CYS B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.227A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.969A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 586 Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.595A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 612 " --> pdb=" O CYS B 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 130 through 157 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.683A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.712A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.436A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 277 removed outlier: 3.535A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.368A pdb=" N THR A 286 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 293 through 312 Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.510A pdb=" N GLY A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.563A pdb=" N THR A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.981A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 481 removed outlier: 3.659A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.521A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 496 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.227A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.971A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.595A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 201 Proline residue: C 167 - end of helix removed outlier: 4.682A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.712A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.438A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 3.534A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.369A pdb=" N THR C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 293 through 312 Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.511A pdb=" N GLY C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.564A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 3.980A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 481 removed outlier: 3.660A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.522A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 496 " --> pdb=" O CYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.226A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.971A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 586 Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.593A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 612 " --> pdb=" O CYS C 608 " (cutoff:3.500A) 992 hydrogen bonds defined for protein. 2931 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: 8.64 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12051 1.03 - 1.23: 27 1.23 - 1.42: 5325 1.42 - 1.62: 7071 1.62 - 1.81: 159 Bond restraints: 24633 Sorted by residual: bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.678 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C11 XMO C 801 " pdb=" O12 XMO C 801 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C10 XMO B 801 " pdb=" C11 XMO B 801 " ideal model delta sigma weight residual 1.534 1.287 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C10 XMO A 801 " pdb=" C11 XMO A 801 " ideal model delta sigma weight residual 1.534 1.288 0.246 2.00e-02 2.50e+03 1.52e+02 ... (remaining 24628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 43768 1.79 - 3.58: 589 3.58 - 5.38: 70 5.38 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 44436 Sorted by residual: angle pdb=" N ASP B 548 " pdb=" CA ASP B 548 " pdb=" C ASP B 548 " ideal model delta sigma weight residual 108.19 103.35 4.84 1.29e+00 6.01e-01 1.41e+01 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 103.35 4.84 1.29e+00 6.01e-01 1.41e+01 angle pdb=" N ASP C 548 " pdb=" CA ASP C 548 " pdb=" C ASP C 548 " ideal model delta sigma weight residual 108.19 103.40 4.79 1.29e+00 6.01e-01 1.38e+01 angle pdb=" C THR B 252 " pdb=" N GLU B 253 " pdb=" CA GLU B 253 " ideal model delta sigma weight residual 119.78 124.07 -4.29 1.24e+00 6.50e-01 1.20e+01 angle pdb=" C THR A 252 " pdb=" N GLU A 253 " pdb=" CA GLU A 253 " ideal model delta sigma weight residual 119.78 124.07 -4.29 1.24e+00 6.50e-01 1.20e+01 ... (remaining 44431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 11306 32.35 - 64.70: 409 64.70 - 97.06: 15 97.06 - 129.41: 3 129.41 - 161.76: 12 Dihedral angle restraints: 11745 sinusoidal: 6015 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO B 801 " pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.16 161.76 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.23 161.69 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C01 XMO A 801 " pdb=" C02 XMO A 801 " pdb=" C04 XMO A 801 " pdb=" O06 XMO A 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.31 161.61 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 11742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1764 0.067 - 0.135: 219 0.135 - 0.202: 0 0.202 - 0.270: 0 0.270 - 0.337: 3 Chirality restraints: 1986 Sorted by residual: chirality pdb=" C10 XMO B 801 " pdb=" C09 XMO B 801 " pdb=" C11 XMO B 801 " pdb=" O22 XMO B 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C10 XMO A 801 " pdb=" C09 XMO A 801 " pdb=" C11 XMO A 801 " pdb=" O22 XMO A 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C10 XMO C 801 " pdb=" C09 XMO C 801 " pdb=" C11 XMO C 801 " pdb=" O22 XMO C 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1983 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 196 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C VAL C 196 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL C 196 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE C 197 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 196 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL B 196 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL B 196 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 196 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL A 196 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 196 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 197 " -0.009 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 942 2.18 - 2.78: 46802 2.78 - 3.39: 67605 3.39 - 3.99: 84316 3.99 - 4.60: 134630 Nonbonded interactions: 334295 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" HG1 THR A 199 " model vdw 1.569 2.450 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.569 2.450 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.573 2.450 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.584 2.450 nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.588 2.450 ... (remaining 334290 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.070 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: 0.420 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 50.950 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.009 0.280 12564 Z= 0.452 Angle : 0.604 8.962 17118 Z= 0.337 Chirality : 0.041 0.337 1986 Planarity : 0.003 0.036 2082 Dihedral : 15.653 161.760 4275 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.72 % Allowed : 4.57 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.31 (0.21), residues: 1593 helix: 2.78 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 316 HIS 0.004 0.001 HIS C 394 PHE 0.012 0.001 PHE A 413 TYR 0.007 0.001 TYR C 519 ARG 0.002 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.14750 ( 992) hydrogen bonds : angle 5.36592 ( 2931) covalent geometry : bond 0.00900 (12564) covalent geometry : angle 0.60375 (17118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 370 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.9005 (t) cc_final: 0.8775 (p) outliers start: 9 outliers final: 3 residues processed: 378 average time/residue: 0.4384 time to fit residues: 251.2575 Evaluate side-chains 213 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 530 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091538 restraints weight = 85625.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095261 restraints weight = 33271.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097599 restraints weight = 18177.181| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12564 Z= 0.155 Angle : 0.559 4.921 17118 Z= 0.304 Chirality : 0.037 0.134 1986 Planarity : 0.003 0.043 2082 Dihedral : 8.104 76.003 1770 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.84 % Allowed : 11.30 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.47 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1329 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.003 0.001 HIS B 132 PHE 0.014 0.001 PHE A 138 TYR 0.009 0.001 TYR A 564 ARG 0.003 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.05468 ( 992) hydrogen bonds : angle 4.59968 ( 2931) covalent geometry : bond 0.00321 (12564) covalent geometry : angle 0.55917 (17118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 497 MET cc_start: 0.8100 (tmt) cc_final: 0.7808 (tmm) REVERT: A 440 GLU cc_start: 0.7737 (tp30) cc_final: 0.7272 (tp30) REVERT: A 497 MET cc_start: 0.8392 (tmt) cc_final: 0.8093 (tmm) REVERT: A 556 MET cc_start: 0.7660 (tpp) cc_final: 0.7413 (mmm) REVERT: C 482 ASP cc_start: 0.8438 (t0) cc_final: 0.8050 (t0) REVERT: C 483 TYR cc_start: 0.7895 (t80) cc_final: 0.7287 (m-80) outliers start: 23 outliers final: 13 residues processed: 230 average time/residue: 0.4062 time to fit residues: 144.6527 Evaluate side-chains 184 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS A 175 HIS ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.084070 restraints weight = 86309.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087529 restraints weight = 34810.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089590 restraints weight = 19488.517| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12564 Z= 0.231 Angle : 0.598 6.503 17118 Z= 0.335 Chirality : 0.038 0.152 1986 Planarity : 0.004 0.039 2082 Dihedral : 6.908 88.553 1770 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.37 % Allowed : 10.42 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.98 (0.21), residues: 1593 helix: 2.54 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.005 0.001 HIS B 367 PHE 0.026 0.002 PHE B 301 TYR 0.013 0.002 TYR B 310 ARG 0.004 0.001 ARG C 163 Details of bonding type rmsd hydrogen bonds : bond 0.06263 ( 992) hydrogen bonds : angle 4.80083 ( 2931) covalent geometry : bond 0.00483 (12564) covalent geometry : angle 0.59780 (17118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 MET cc_start: 0.8486 (tmt) cc_final: 0.8273 (tmm) REVERT: C 283 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: C 365 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8296 (mp0) outliers start: 42 outliers final: 31 residues processed: 203 average time/residue: 0.3721 time to fit residues: 121.7737 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.104601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083646 restraints weight = 88503.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087100 restraints weight = 34280.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089247 restraints weight = 19070.873| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12564 Z= 0.169 Angle : 0.510 4.617 17118 Z= 0.281 Chirality : 0.035 0.115 1986 Planarity : 0.003 0.040 2082 Dihedral : 6.114 76.456 1770 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.80 % Allowed : 12.34 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.26 (0.21), residues: 1593 helix: 2.76 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.003 0.001 HIS A 367 PHE 0.012 0.001 PHE B 221 TYR 0.012 0.001 TYR B 564 ARG 0.002 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.05129 ( 992) hydrogen bonds : angle 4.49254 ( 2931) covalent geometry : bond 0.00363 (12564) covalent geometry : angle 0.50950 (17118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8851 (mt) cc_final: 0.8634 (tt) REVERT: A 257 MET cc_start: 0.7229 (tmm) cc_final: 0.6930 (tmm) REVERT: A 556 MET cc_start: 0.8122 (mmm) cc_final: 0.7902 (mmm) outliers start: 35 outliers final: 27 residues processed: 181 average time/residue: 0.3813 time to fit residues: 111.1735 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 155 optimal weight: 3.9990 chunk 34 optimal weight: 0.0020 chunk 27 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 1.4792 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.105802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084887 restraints weight = 87740.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088425 restraints weight = 33986.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090603 restraints weight = 18863.341| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12564 Z= 0.128 Angle : 0.477 7.426 17118 Z= 0.256 Chirality : 0.034 0.125 1986 Planarity : 0.003 0.041 2082 Dihedral : 5.514 70.768 1770 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.24 % Allowed : 13.30 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.53 (0.21), residues: 1593 helix: 2.96 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.002 0.001 HIS B 367 PHE 0.020 0.001 PHE A 221 TYR 0.010 0.001 TYR B 564 ARG 0.002 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 992) hydrogen bonds : angle 4.20703 ( 2931) covalent geometry : bond 0.00265 (12564) covalent geometry : angle 0.47676 (17118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 MET cc_start: 0.7376 (mtt) cc_final: 0.7155 (mtt) REVERT: A 257 MET cc_start: 0.7247 (tmm) cc_final: 0.6917 (tmm) REVERT: C 283 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7390 (mp0) outliers start: 28 outliers final: 22 residues processed: 171 average time/residue: 0.4182 time to fit residues: 115.7735 Evaluate side-chains 161 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.104962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084098 restraints weight = 87950.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087551 restraints weight = 34301.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089681 restraints weight = 19218.973| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12564 Z= 0.138 Angle : 0.475 7.314 17118 Z= 0.256 Chirality : 0.034 0.113 1986 Planarity : 0.003 0.041 2082 Dihedral : 5.279 65.066 1764 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.32 % Allowed : 13.46 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.54 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.05 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.003 0.001 HIS A 367 PHE 0.018 0.001 PHE C 221 TYR 0.010 0.001 TYR B 564 ARG 0.001 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 992) hydrogen bonds : angle 4.17022 ( 2931) covalent geometry : bond 0.00293 (12564) covalent geometry : angle 0.47503 (17118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7377 (tmm) cc_final: 0.7048 (tmm) REVERT: A 325 MET cc_start: 0.8855 (ttm) cc_final: 0.8648 (ttm) REVERT: C 283 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7479 (mp0) outliers start: 29 outliers final: 25 residues processed: 173 average time/residue: 0.3956 time to fit residues: 110.3079 Evaluate side-chains 164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 129 optimal weight: 0.0570 chunk 104 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082385 restraints weight = 88849.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085806 restraints weight = 34742.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087895 restraints weight = 19442.089| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12564 Z= 0.178 Angle : 0.509 7.336 17118 Z= 0.280 Chirality : 0.035 0.118 1986 Planarity : 0.004 0.040 2082 Dihedral : 5.485 65.786 1764 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.56 % Allowed : 14.02 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.28 (0.21), residues: 1593 helix: 2.80 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.15 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.018 0.002 PHE C 501 TYR 0.013 0.001 TYR C 564 ARG 0.002 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 992) hydrogen bonds : angle 4.34993 ( 2931) covalent geometry : bond 0.00383 (12564) covalent geometry : angle 0.50880 (17118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7411 (tmm) cc_final: 0.7079 (tmm) REVERT: A 325 MET cc_start: 0.8860 (ttm) cc_final: 0.8608 (ttm) outliers start: 32 outliers final: 27 residues processed: 170 average time/residue: 0.4033 time to fit residues: 109.3091 Evaluate side-chains 163 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083401 restraints weight = 88317.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086856 restraints weight = 34238.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089011 restraints weight = 19048.644| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12564 Z= 0.142 Angle : 0.483 7.822 17118 Z= 0.260 Chirality : 0.034 0.120 1986 Planarity : 0.003 0.043 2082 Dihedral : 5.171 65.663 1764 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.32 % Allowed : 14.82 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.42 (0.21), residues: 1593 helix: 2.92 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.016 0.001 PHE C 221 TYR 0.012 0.001 TYR B 564 ARG 0.001 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 992) hydrogen bonds : angle 4.16141 ( 2931) covalent geometry : bond 0.00302 (12564) covalent geometry : angle 0.48346 (17118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7366 (tmm) cc_final: 0.7032 (tmm) outliers start: 29 outliers final: 28 residues processed: 169 average time/residue: 0.4065 time to fit residues: 111.6382 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 21 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.102773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.082151 restraints weight = 89215.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085527 restraints weight = 34659.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087602 restraints weight = 19385.599| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12564 Z= 0.175 Angle : 0.509 8.083 17118 Z= 0.278 Chirality : 0.035 0.120 1986 Planarity : 0.003 0.041 2082 Dihedral : 5.378 64.732 1764 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.48 % Allowed : 14.66 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.21 (0.21), residues: 1593 helix: 2.78 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.34 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.030 0.002 PHE C 301 TYR 0.012 0.001 TYR C 564 ARG 0.001 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 992) hydrogen bonds : angle 4.31434 ( 2931) covalent geometry : bond 0.00377 (12564) covalent geometry : angle 0.50877 (17118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7418 (tmm) cc_final: 0.7084 (tmm) REVERT: A 501 PHE cc_start: 0.8868 (t80) cc_final: 0.8638 (t80) REVERT: C 205 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8217 (mp10) outliers start: 31 outliers final: 29 residues processed: 167 average time/residue: 0.3679 time to fit residues: 99.7913 Evaluate side-chains 169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.103442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082873 restraints weight = 88517.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086328 restraints weight = 34396.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088460 restraints weight = 19118.707| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12564 Z= 0.150 Angle : 0.492 8.595 17118 Z= 0.266 Chirality : 0.035 0.126 1986 Planarity : 0.003 0.042 2082 Dihedral : 5.194 64.916 1764 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.40 % Allowed : 15.30 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.25 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.004 0.001 HIS B 367 PHE 0.024 0.001 PHE C 301 TYR 0.013 0.001 TYR B 564 ARG 0.002 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 992) hydrogen bonds : angle 4.22136 ( 2931) covalent geometry : bond 0.00323 (12564) covalent geometry : angle 0.49215 (17118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7399 (tmm) cc_final: 0.7056 (tmm) REVERT: C 205 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: C 377 ILE cc_start: 0.8684 (pt) cc_final: 0.8445 (pt) outliers start: 30 outliers final: 27 residues processed: 168 average time/residue: 0.3926 time to fit residues: 107.2460 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.104572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084163 restraints weight = 87731.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087666 restraints weight = 33780.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089796 restraints weight = 18640.577| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12564 Z= 0.121 Angle : 0.472 8.640 17118 Z= 0.252 Chirality : 0.034 0.126 1986 Planarity : 0.003 0.044 2082 Dihedral : 4.911 62.512 1764 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 15.95 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.43 (0.21), residues: 1593 helix: 2.97 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.40 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS B 367 PHE 0.029 0.001 PHE A 221 TYR 0.010 0.001 TYR B 564 ARG 0.002 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 992) hydrogen bonds : angle 4.04146 ( 2931) covalent geometry : bond 0.00258 (12564) covalent geometry : angle 0.47165 (17118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6597.96 seconds wall clock time: 113 minutes 40.76 seconds (6820.76 seconds total)