Starting phenix.real_space_refine on Sat Aug 23 04:57:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c77_30294/08_2025/7c77_30294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c77_30294/08_2025/7c77_30294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c77_30294/08_2025/7c77_30294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c77_30294/08_2025/7c77_30294.map" model { file = "/net/cci-nas-00/data/ceres_data/7c77_30294/08_2025/7c77_30294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c77_30294/08_2025/7c77_30294.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6317 2.51 5 N 1603 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5616 Classifications: {'peptide': 700} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 670} Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3869 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 21, 'TRANS': 461} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.02, per 1000 atoms: 0.21 Number of scatterers: 9762 At special positions: 0 Unit cell: (136.95, 171.81, 94.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1806 8.00 N 1603 7.00 C 6317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 678 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 368 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1001 " - " ASN A 58 " " NAG A1002 " - " ASN A 125 " " NAG A1003 " - " ASN A 197 " " NAG A1004 " - " ASN A 248 " " NAG A1005 " - " ASN A 253 " " NAG A1006 " - " ASN A 292 " " NAG A1016 " - " ASN A 668 " " NAG A1017 " - " ASN A 663 " " NAG B 601 " - " ASN B 251 " " NAG C 1 " - " ASN A 414 " " NAG D 1 " - " ASN A 425 " " NAG E 1 " - " ASN A 399 " " NAG F 1 " - " ASN A 508 " " NAG G 1 " - " ASN B 272 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 429.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 40.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.032A pdb=" N THR A 73 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 74 " --> pdb=" O ASN A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.899A pdb=" N GLN A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.747A pdb=" N LEU A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.617A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.771A pdb=" N LYS A 273 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.845A pdb=" N TRP A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.818A pdb=" N TRP A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Proline residue: A 633 - end of helix removed outlier: 4.530A pdb=" N ASN A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 removed outlier: 6.437A pdb=" N TRP A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.669A pdb=" N HIS A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 676' Processing helix chain 'A' and resid 702 through 727 removed outlier: 3.562A pdb=" N ILE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 89 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.667A pdb=" N THR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.622A pdb=" N MET B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 199 Proline residue: B 163 - end of helix removed outlier: 4.841A pdb=" N VAL B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 213 through 235 removed outlier: 3.986A pdb=" N VAL B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.846A pdb=" N THR B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 307 Processing helix chain 'B' and resid 312 through 321 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 339 through 359 Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 374 through 395 removed outlier: 3.726A pdb=" N VAL B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.053A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 461 removed outlier: 3.826A pdb=" N TYR B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 488 Processing helix chain 'B' and resid 494 through 517 removed outlier: 3.842A pdb=" N ALA B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 517 " --> pdb=" O TRP B 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.475A pdb=" N LEU A 57 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N SER A 199 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ALA A 226 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG A 201 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU A 228 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 203 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 486 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 592 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 616 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.929A pdb=" N LEU A 187 " --> pdb=" O GLU A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 264 removed outlier: 3.888A pdb=" N THR A 264 " --> pdb=" O ASP A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.747A pdb=" N LEU A 314 " --> pdb=" O ASN A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.712A pdb=" N GLN A 471 " --> pdb=" O GLN A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 648 through 649 removed outlier: 7.343A pdb=" N LEU A 677 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 687 " --> pdb=" O CYS A 678 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3018 1.34 - 1.46: 1809 1.46 - 1.58: 5107 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 9991 Sorted by residual: bond pdb=" N ALA B 506 " pdb=" CA ALA B 506 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.19e-02 7.06e+03 6.48e+00 bond pdb=" CA ALA B 506 " pdb=" C ALA B 506 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.27e-02 6.20e+03 4.33e+00 bond pdb=" C ALA B 506 " pdb=" O ALA B 506 " ideal model delta sigma weight residual 1.236 1.257 -0.021 1.15e-02 7.56e+03 3.21e+00 bond pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.01e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.48e+00 ... (remaining 9986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 12932 1.41 - 2.81: 526 2.81 - 4.22: 83 4.22 - 5.62: 31 5.62 - 7.03: 8 Bond angle restraints: 13580 Sorted by residual: angle pdb=" C SER B 510 " pdb=" N TYR B 511 " pdb=" CA TYR B 511 " ideal model delta sigma weight residual 120.54 124.87 -4.33 1.35e+00 5.49e-01 1.03e+01 angle pdb=" CA GLY B 266 " pdb=" C GLY B 266 " pdb=" N ILE B 267 " ideal model delta sigma weight residual 114.23 116.75 -2.52 8.80e-01 1.29e+00 8.17e+00 angle pdb=" CA SER B 510 " pdb=" C SER B 510 " pdb=" N TYR B 511 " ideal model delta sigma weight residual 117.39 114.08 3.31 1.24e+00 6.50e-01 7.14e+00 angle pdb=" C TRP A 547 " pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.69e+00 angle pdb=" CA VAL B 275 " pdb=" C VAL B 275 " pdb=" N LEU B 276 " ideal model delta sigma weight residual 116.60 120.16 -3.56 1.45e+00 4.76e-01 6.04e+00 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 5534 21.71 - 43.42: 568 43.42 - 65.13: 74 65.13 - 86.85: 22 86.85 - 108.56: 4 Dihedral angle restraints: 6202 sinusoidal: 2730 harmonic: 3472 Sorted by residual: dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 38 " pdb=" CB CYS A 38 " ideal model delta sinusoidal sigma weight residual -86.00 -24.67 -61.33 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual -86.00 -51.65 -34.35 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CB CYS B 260 " pdb=" SG CYS B 260 " pdb=" SG CYS B 368 " pdb=" CB CYS B 368 " ideal model delta sinusoidal sigma weight residual 93.00 125.81 -32.81 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 6199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1364 0.055 - 0.109: 226 0.109 - 0.163: 21 0.163 - 0.218: 1 0.218 - 0.272: 1 Chirality restraints: 1613 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C2 NAG A1002 " pdb=" C1 NAG A1002 " pdb=" C3 NAG A1002 " pdb=" N2 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1610 not shown) Planarity restraints: 1694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 207 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO B 208 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 506 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C ALA B 506 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA B 506 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 507 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 118 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 119 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.025 5.00e-02 4.00e+02 ... (remaining 1691 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 969 2.75 - 3.29: 9757 3.29 - 3.82: 16278 3.82 - 4.36: 18331 4.36 - 4.90: 31933 Nonbonded interactions: 77268 Sorted by model distance: nonbonded pdb=" OH TYR B 248 " pdb=" O THR B 274 " model vdw 2.209 3.040 nonbonded pdb=" O SER A 373 " pdb=" OG SER A 404 " model vdw 2.269 3.040 nonbonded pdb=" O SER A 475 " pdb=" OG SER A 475 " model vdw 2.292 3.040 nonbonded pdb=" O HIS B 229 " pdb=" OG SER B 383 " model vdw 2.292 3.040 nonbonded pdb=" O ALA B 222 " pdb=" OG SER B 390 " model vdw 2.304 3.040 ... (remaining 77263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.003 0.035 10016 Z= 0.176 Angle : 0.670 7.030 13650 Z= 0.341 Chirality : 0.041 0.272 1613 Planarity : 0.004 0.065 1680 Dihedral : 16.649 108.557 3945 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 1.88 % Allowed : 12.15 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.22), residues: 1179 helix: -0.89 (0.23), residues: 415 sheet: -1.91 (0.48), residues: 121 loop : -2.35 (0.21), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 466 TYR 0.017 0.001 TYR B 511 PHE 0.016 0.001 PHE A 692 TRP 0.007 0.001 TRP A 547 HIS 0.005 0.000 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9991) covalent geometry : angle 0.66767 (13580) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.41810 ( 10) hydrogen bonds : bond 0.15399 ( 348) hydrogen bonds : angle 5.70740 ( 1032) link_BETA1-4 : bond 0.00333 ( 6) link_BETA1-4 : angle 1.26186 ( 18) link_NAG-ASN : bond 0.00214 ( 14) link_NAG-ASN : angle 0.98377 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 334 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8210 (mtmm) REVERT: A 364 ASP cc_start: 0.7916 (m-30) cc_final: 0.7662 (m-30) REVERT: A 365 ASP cc_start: 0.8190 (t0) cc_final: 0.7942 (t0) REVERT: A 398 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 448 LEU cc_start: 0.9238 (mt) cc_final: 0.9028 (mt) REVERT: A 660 ASN cc_start: 0.8055 (m-40) cc_final: 0.7853 (m-40) REVERT: B 478 GLN cc_start: 0.7325 (tt0) cc_final: 0.7019 (tt0) outliers start: 20 outliers final: 8 residues processed: 344 average time/residue: 0.0754 time to fit residues: 38.5042 Evaluate side-chains 294 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 285 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 110 ASN A 182 ASN A 344 HIS A 418 ASN A 619 GLN B 412 HIS ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.145429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121265 restraints weight = 16830.604| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.75 r_work: 0.3522 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 10016 Z= 0.244 Angle : 0.764 9.691 13650 Z= 0.368 Chirality : 0.048 0.234 1613 Planarity : 0.005 0.047 1680 Dihedral : 7.778 65.040 1709 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.80 % Allowed : 20.15 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.24), residues: 1179 helix: 0.07 (0.25), residues: 445 sheet: -1.66 (0.48), residues: 116 loop : -1.64 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 490 TYR 0.020 0.002 TYR A 303 PHE 0.025 0.002 PHE B 347 TRP 0.014 0.001 TRP B 476 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 9991) covalent geometry : angle 0.75725 (13580) SS BOND : bond 0.00401 ( 5) SS BOND : angle 0.82778 ( 10) hydrogen bonds : bond 0.04918 ( 348) hydrogen bonds : angle 4.71470 ( 1032) link_BETA1-4 : bond 0.00379 ( 6) link_BETA1-4 : angle 2.09832 ( 18) link_NAG-ASN : bond 0.00368 ( 14) link_NAG-ASN : angle 1.53814 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8093 (t0) cc_final: 0.7743 (t0) REVERT: A 183 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8143 (mtmm) REVERT: A 330 LEU cc_start: 0.9210 (mm) cc_final: 0.9006 (mp) REVERT: A 364 ASP cc_start: 0.7954 (m-30) cc_final: 0.7702 (m-30) REVERT: A 494 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8138 (mmmt) REVERT: A 545 ARG cc_start: 0.8470 (tpm170) cc_final: 0.8035 (tpm170) REVERT: A 627 GLU cc_start: 0.8153 (mp0) cc_final: 0.7897 (mp0) REVERT: A 644 ARG cc_start: 0.8790 (ptt90) cc_final: 0.8252 (ptt-90) REVERT: B 189 LYS cc_start: 0.8466 (ttmm) cc_final: 0.7976 (mptt) REVERT: B 243 LEU cc_start: 0.9186 (tp) cc_final: 0.8985 (tt) REVERT: B 297 PHE cc_start: 0.8385 (t80) cc_final: 0.8149 (t80) REVERT: B 441 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8875 (mp) REVERT: B 478 GLN cc_start: 0.8422 (tt0) cc_final: 0.7977 (tt0) outliers start: 51 outliers final: 37 residues processed: 323 average time/residue: 0.0798 time to fit residues: 37.7732 Evaluate side-chains 306 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 505 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 344 HIS A 610 GLN B 195 HIS B 244 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122821 restraints weight = 16696.000| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.71 r_work: 0.3550 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10016 Z= 0.146 Angle : 0.664 12.372 13650 Z= 0.316 Chirality : 0.045 0.233 1613 Planarity : 0.004 0.049 1680 Dihedral : 6.691 56.506 1706 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.24 % Allowed : 23.26 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.24), residues: 1179 helix: 0.34 (0.25), residues: 444 sheet: -1.44 (0.50), residues: 116 loop : -1.46 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.019 0.002 TYR B 158 PHE 0.034 0.001 PHE B 347 TRP 0.010 0.001 TRP B 476 HIS 0.009 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9991) covalent geometry : angle 0.65630 (13580) SS BOND : bond 0.00543 ( 5) SS BOND : angle 2.06281 ( 10) hydrogen bonds : bond 0.04367 ( 348) hydrogen bonds : angle 4.46430 ( 1032) link_BETA1-4 : bond 0.00412 ( 6) link_BETA1-4 : angle 1.77104 ( 18) link_NAG-ASN : bond 0.00156 ( 14) link_NAG-ASN : angle 1.24869 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8077 (t0) cc_final: 0.7723 (t0) REVERT: A 173 ASN cc_start: 0.8765 (m-40) cc_final: 0.8476 (m110) REVERT: A 183 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8163 (mtmm) REVERT: A 195 LEU cc_start: 0.8820 (mt) cc_final: 0.8485 (mp) REVERT: A 493 LEU cc_start: 0.9121 (tp) cc_final: 0.8858 (tp) REVERT: A 494 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8036 (mmmt) REVERT: A 545 ARG cc_start: 0.8472 (tpm170) cc_final: 0.8151 (tpm170) REVERT: A 627 GLU cc_start: 0.8167 (mp0) cc_final: 0.7840 (mp0) REVERT: A 644 ARG cc_start: 0.8774 (ptt90) cc_final: 0.8287 (ptt-90) REVERT: B 75 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8156 (t80) REVERT: B 186 MET cc_start: 0.8792 (tpp) cc_final: 0.8139 (ttp) REVERT: B 189 LYS cc_start: 0.8462 (ttmm) cc_final: 0.7951 (mptt) REVERT: B 244 ASN cc_start: 0.8719 (m110) cc_final: 0.8370 (m110) REVERT: B 297 PHE cc_start: 0.8444 (t80) cc_final: 0.8169 (t80) REVERT: B 370 MET cc_start: 0.7513 (pmm) cc_final: 0.7142 (pmm) REVERT: B 441 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 478 GLN cc_start: 0.8312 (tt0) cc_final: 0.7931 (tt0) outliers start: 45 outliers final: 30 residues processed: 319 average time/residue: 0.0713 time to fit residues: 33.7031 Evaluate side-chains 312 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 505 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS A 646 ASN B 83 GLN B 195 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122922 restraints weight = 16936.737| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.80 r_work: 0.3551 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10016 Z= 0.120 Angle : 0.638 10.649 13650 Z= 0.302 Chirality : 0.044 0.239 1613 Planarity : 0.004 0.051 1680 Dihedral : 5.815 56.468 1704 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.58 % Favored : 95.34 % Rotamer: Outliers : 5.56 % Allowed : 23.26 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1179 helix: 0.57 (0.25), residues: 443 sheet: -1.43 (0.50), residues: 116 loop : -1.33 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.020 0.001 TYR B 158 PHE 0.035 0.001 PHE B 347 TRP 0.009 0.001 TRP B 476 HIS 0.009 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9991) covalent geometry : angle 0.63204 (13580) SS BOND : bond 0.00322 ( 5) SS BOND : angle 1.46184 ( 10) hydrogen bonds : bond 0.03976 ( 348) hydrogen bonds : angle 4.37161 ( 1032) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 1.65539 ( 18) link_NAG-ASN : bond 0.00164 ( 14) link_NAG-ASN : angle 1.19859 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8067 (t0) cc_final: 0.7748 (t0) REVERT: A 173 ASN cc_start: 0.8768 (m-40) cc_final: 0.8476 (m110) REVERT: A 183 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8206 (mtmm) REVERT: A 195 LEU cc_start: 0.8829 (mt) cc_final: 0.8599 (mp) REVERT: A 388 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 464 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 471 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8050 (mm110) REVERT: A 493 LEU cc_start: 0.9144 (tp) cc_final: 0.8911 (tp) REVERT: A 494 LYS cc_start: 0.8656 (mmmm) cc_final: 0.7948 (mmmt) REVERT: A 519 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8173 (pt) REVERT: A 545 ARG cc_start: 0.8536 (tpm170) cc_final: 0.8192 (tpm170) REVERT: A 644 ARG cc_start: 0.8707 (ptt90) cc_final: 0.8377 (ptt-90) REVERT: A 645 PHE cc_start: 0.8590 (m-80) cc_final: 0.8138 (m-80) REVERT: B 75 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7985 (t80) REVERT: B 186 MET cc_start: 0.8606 (tpp) cc_final: 0.8001 (ttp) REVERT: B 189 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7902 (mptt) REVERT: B 297 PHE cc_start: 0.8423 (t80) cc_final: 0.8104 (t80) REVERT: B 370 MET cc_start: 0.7689 (pmm) cc_final: 0.7247 (pmm) REVERT: B 441 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 478 GLN cc_start: 0.8251 (tt0) cc_final: 0.7782 (tt0) outliers start: 59 outliers final: 34 residues processed: 321 average time/residue: 0.0846 time to fit residues: 39.7987 Evaluate side-chains 319 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 344 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.143508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.119889 restraints weight = 16885.905| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.66 r_work: 0.3497 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10016 Z= 0.180 Angle : 0.680 10.488 13650 Z= 0.326 Chirality : 0.045 0.238 1613 Planarity : 0.004 0.051 1680 Dihedral : 5.838 58.810 1702 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 5.65 % Allowed : 24.76 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.25), residues: 1179 helix: 0.63 (0.25), residues: 443 sheet: -1.51 (0.50), residues: 118 loop : -1.27 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 490 TYR 0.019 0.002 TYR B 158 PHE 0.036 0.002 PHE B 347 TRP 0.014 0.001 TRP B 476 HIS 0.006 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9991) covalent geometry : angle 0.67116 (13580) SS BOND : bond 0.00423 ( 5) SS BOND : angle 2.79721 ( 10) hydrogen bonds : bond 0.04293 ( 348) hydrogen bonds : angle 4.43046 ( 1032) link_BETA1-4 : bond 0.00310 ( 6) link_BETA1-4 : angle 1.66711 ( 18) link_NAG-ASN : bond 0.00214 ( 14) link_NAG-ASN : angle 1.28952 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8138 (t0) cc_final: 0.7801 (t0) REVERT: A 173 ASN cc_start: 0.8781 (m-40) cc_final: 0.8491 (m110) REVERT: A 183 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8350 (mmmm) REVERT: A 195 LEU cc_start: 0.8946 (mt) cc_final: 0.8661 (mp) REVERT: A 246 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 388 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8351 (p) REVERT: A 471 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8101 (mm110) REVERT: A 493 LEU cc_start: 0.9110 (tp) cc_final: 0.8876 (tp) REVERT: A 494 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8007 (mmmt) REVERT: A 514 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8455 (pt) REVERT: A 519 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8233 (pt) REVERT: A 627 GLU cc_start: 0.8136 (mp0) cc_final: 0.7899 (mp0) REVERT: A 644 ARG cc_start: 0.8778 (ptt90) cc_final: 0.8374 (ptt-90) REVERT: A 645 PHE cc_start: 0.8529 (m-80) cc_final: 0.8056 (m-80) REVERT: B 75 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8121 (t80) REVERT: B 186 MET cc_start: 0.8731 (tpp) cc_final: 0.8033 (ttp) REVERT: B 189 LYS cc_start: 0.8492 (ttmm) cc_final: 0.7979 (mptt) REVERT: B 297 PHE cc_start: 0.8694 (t80) cc_final: 0.8425 (t80) REVERT: B 361 PHE cc_start: 0.8921 (t80) cc_final: 0.8446 (t80) REVERT: B 441 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8883 (mp) outliers start: 60 outliers final: 41 residues processed: 317 average time/residue: 0.0745 time to fit residues: 34.7365 Evaluate side-chains 323 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.144062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119765 restraints weight = 16924.358| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.75 r_work: 0.3522 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10016 Z= 0.130 Angle : 0.661 9.894 13650 Z= 0.311 Chirality : 0.044 0.237 1613 Planarity : 0.004 0.050 1680 Dihedral : 5.516 58.984 1700 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.58 % Favored : 95.34 % Rotamer: Outliers : 5.18 % Allowed : 25.80 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.25), residues: 1179 helix: 0.74 (0.25), residues: 442 sheet: -1.53 (0.50), residues: 118 loop : -1.21 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.020 0.001 TYR B 158 PHE 0.034 0.001 PHE B 347 TRP 0.010 0.001 TRP B 476 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9991) covalent geometry : angle 0.65508 (13580) SS BOND : bond 0.00374 ( 5) SS BOND : angle 1.66945 ( 10) hydrogen bonds : bond 0.04042 ( 348) hydrogen bonds : angle 4.35235 ( 1032) link_BETA1-4 : bond 0.00428 ( 6) link_BETA1-4 : angle 1.50503 ( 18) link_NAG-ASN : bond 0.00152 ( 14) link_NAG-ASN : angle 1.19783 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8168 (t0) cc_final: 0.7849 (t0) REVERT: A 103 LYS cc_start: 0.7906 (ptpt) cc_final: 0.7542 (mptt) REVERT: A 173 ASN cc_start: 0.8778 (m-40) cc_final: 0.8494 (m110) REVERT: A 183 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8344 (mmmm) REVERT: A 266 GLU cc_start: 0.8449 (tt0) cc_final: 0.8036 (tt0) REVERT: A 388 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 471 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8062 (mm110) REVERT: A 519 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8277 (pt) REVERT: A 531 GLU cc_start: 0.8778 (mp0) cc_final: 0.8556 (mp0) REVERT: A 545 ARG cc_start: 0.8168 (tpt90) cc_final: 0.7895 (tpt90) REVERT: A 644 ARG cc_start: 0.8736 (ptt90) cc_final: 0.8317 (ptt-90) REVERT: A 645 PHE cc_start: 0.8496 (m-80) cc_final: 0.8004 (m-80) REVERT: B 75 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7782 (t80) REVERT: B 138 MET cc_start: 0.8648 (tmm) cc_final: 0.8198 (tmm) REVERT: B 179 MET cc_start: 0.9127 (tpp) cc_final: 0.8595 (tpp) REVERT: B 186 MET cc_start: 0.8758 (tpp) cc_final: 0.8068 (ttp) REVERT: B 189 LYS cc_start: 0.8530 (ttmm) cc_final: 0.7998 (mptt) REVERT: B 243 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8800 (tt) REVERT: B 297 PHE cc_start: 0.8726 (t80) cc_final: 0.8470 (t80) REVERT: B 316 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7545 (tp30) REVERT: B 361 PHE cc_start: 0.8897 (t80) cc_final: 0.8380 (t80) REVERT: B 365 TYR cc_start: 0.8721 (m-10) cc_final: 0.8422 (m-10) REVERT: B 441 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8907 (mp) REVERT: B 478 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7989 (tt0) outliers start: 55 outliers final: 39 residues processed: 315 average time/residue: 0.0722 time to fit residues: 33.6129 Evaluate side-chains 322 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116848 restraints weight = 16740.805| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.63 r_work: 0.3469 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10016 Z= 0.214 Angle : 0.716 9.930 13650 Z= 0.341 Chirality : 0.047 0.234 1613 Planarity : 0.004 0.050 1680 Dihedral : 5.690 59.104 1699 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 5.93 % Allowed : 26.46 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.25), residues: 1179 helix: 0.82 (0.26), residues: 431 sheet: -1.62 (0.50), residues: 118 loop : -1.14 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.020 0.002 TYR B 158 PHE 0.034 0.002 PHE B 347 TRP 0.017 0.001 TRP B 476 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9991) covalent geometry : angle 0.71011 (13580) SS BOND : bond 0.00434 ( 5) SS BOND : angle 1.52621 ( 10) hydrogen bonds : bond 0.04483 ( 348) hydrogen bonds : angle 4.46978 ( 1032) link_BETA1-4 : bond 0.00411 ( 6) link_BETA1-4 : angle 1.67360 ( 18) link_NAG-ASN : bond 0.00276 ( 14) link_NAG-ASN : angle 1.35598 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8192 (t0) cc_final: 0.7868 (t0) REVERT: A 173 ASN cc_start: 0.8787 (m-40) cc_final: 0.8536 (m110) REVERT: A 183 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8377 (mmmm) REVERT: A 266 GLU cc_start: 0.8476 (tt0) cc_final: 0.8059 (tt0) REVERT: A 388 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8440 (p) REVERT: A 471 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8062 (mm110) REVERT: A 494 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8132 (mmmt) REVERT: A 514 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8553 (pt) REVERT: A 519 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8300 (pt) REVERT: A 531 GLU cc_start: 0.8817 (mp0) cc_final: 0.8588 (mp0) REVERT: A 545 ARG cc_start: 0.8202 (tpt90) cc_final: 0.7908 (tpt90) REVERT: A 627 GLU cc_start: 0.8043 (mp0) cc_final: 0.7729 (mp0) REVERT: A 644 ARG cc_start: 0.8790 (ptt90) cc_final: 0.8204 (ptt-90) REVERT: B 75 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8071 (t80) REVERT: B 138 MET cc_start: 0.8668 (tmm) cc_final: 0.8205 (tmm) REVERT: B 186 MET cc_start: 0.8724 (tpp) cc_final: 0.8045 (ttp) REVERT: B 189 LYS cc_start: 0.8488 (ttmm) cc_final: 0.7962 (mptt) REVERT: B 243 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8821 (tt) REVERT: B 297 PHE cc_start: 0.8853 (t80) cc_final: 0.8624 (t80) REVERT: B 316 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: B 370 MET cc_start: 0.7576 (pmm) cc_final: 0.7330 (pmm) REVERT: B 441 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8903 (mp) outliers start: 63 outliers final: 44 residues processed: 309 average time/residue: 0.0674 time to fit residues: 30.9711 Evaluate side-chains 320 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.143404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119662 restraints weight = 16601.890| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.60 r_work: 0.3496 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10016 Z= 0.140 Angle : 0.702 11.537 13650 Z= 0.329 Chirality : 0.045 0.234 1613 Planarity : 0.004 0.052 1680 Dihedral : 5.525 58.417 1699 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 5.65 % Allowed : 27.50 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.25), residues: 1179 helix: 0.75 (0.25), residues: 437 sheet: -1.62 (0.51), residues: 118 loop : -1.10 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 65 TYR 0.022 0.001 TYR B 158 PHE 0.035 0.001 PHE B 347 TRP 0.014 0.001 TRP B 137 HIS 0.015 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9991) covalent geometry : angle 0.69780 (13580) SS BOND : bond 0.00330 ( 5) SS BOND : angle 1.24011 ( 10) hydrogen bonds : bond 0.04266 ( 348) hydrogen bonds : angle 4.45574 ( 1032) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 1.51931 ( 18) link_NAG-ASN : bond 0.00165 ( 14) link_NAG-ASN : angle 1.23897 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8121 (p0) cc_final: 0.7872 (p0) REVERT: A 82 ASP cc_start: 0.8190 (t0) cc_final: 0.7810 (t0) REVERT: A 173 ASN cc_start: 0.8769 (m-40) cc_final: 0.8520 (m110) REVERT: A 183 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8364 (mmmm) REVERT: A 266 GLU cc_start: 0.8450 (tt0) cc_final: 0.8007 (tt0) REVERT: A 388 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 439 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 471 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7960 (mm110) REVERT: A 494 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8047 (mmmt) REVERT: A 519 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8315 (pt) REVERT: A 531 GLU cc_start: 0.8752 (mp0) cc_final: 0.8527 (mp0) REVERT: A 627 GLU cc_start: 0.7998 (mp0) cc_final: 0.7676 (mp0) REVERT: A 644 ARG cc_start: 0.8745 (ptt90) cc_final: 0.8312 (ptt-90) REVERT: A 645 PHE cc_start: 0.8518 (m-80) cc_final: 0.8026 (m-80) REVERT: A 713 MET cc_start: 0.7790 (tmm) cc_final: 0.7474 (tmm) REVERT: A 725 HIS cc_start: 0.7805 (t-90) cc_final: 0.7513 (t-90) REVERT: B 75 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7627 (t80) REVERT: B 132 PHE cc_start: 0.8760 (t80) cc_final: 0.8544 (t80) REVERT: B 138 MET cc_start: 0.8593 (tmm) cc_final: 0.8353 (tmm) REVERT: B 186 MET cc_start: 0.8783 (tpp) cc_final: 0.8080 (ttp) REVERT: B 189 LYS cc_start: 0.8500 (ttmm) cc_final: 0.7984 (mptt) REVERT: B 243 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 297 PHE cc_start: 0.8806 (t80) cc_final: 0.8584 (t80) REVERT: B 316 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: B 370 MET cc_start: 0.7559 (pmm) cc_final: 0.7310 (pmm) REVERT: B 441 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8884 (mp) outliers start: 60 outliers final: 38 residues processed: 318 average time/residue: 0.0715 time to fit residues: 33.8182 Evaluate side-chains 319 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.118467 restraints weight = 16789.487| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.60 r_work: 0.3490 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10016 Z= 0.150 Angle : 0.713 10.919 13650 Z= 0.333 Chirality : 0.045 0.234 1613 Planarity : 0.004 0.053 1680 Dihedral : 5.495 57.663 1699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 4.80 % Allowed : 28.25 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.25), residues: 1179 helix: 0.76 (0.25), residues: 436 sheet: -1.69 (0.50), residues: 118 loop : -1.05 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 65 TYR 0.022 0.001 TYR B 158 PHE 0.035 0.002 PHE B 347 TRP 0.016 0.001 TRP B 137 HIS 0.014 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9991) covalent geometry : angle 0.70832 (13580) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.39376 ( 10) hydrogen bonds : bond 0.04303 ( 348) hydrogen bonds : angle 4.50091 ( 1032) link_BETA1-4 : bond 0.00363 ( 6) link_BETA1-4 : angle 1.59008 ( 18) link_NAG-ASN : bond 0.00194 ( 14) link_NAG-ASN : angle 1.26697 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8136 (tp) cc_final: 0.7933 (tt) REVERT: A 82 ASP cc_start: 0.8230 (t0) cc_final: 0.7829 (t0) REVERT: A 95 LEU cc_start: 0.9250 (tp) cc_final: 0.9007 (mm) REVERT: A 173 ASN cc_start: 0.8816 (m-40) cc_final: 0.8575 (m110) REVERT: A 183 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8380 (mmmm) REVERT: A 266 GLU cc_start: 0.8504 (tt0) cc_final: 0.8090 (tt0) REVERT: A 388 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8502 (p) REVERT: A 471 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8067 (mm110) REVERT: A 494 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8077 (mmmt) REVERT: A 519 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8346 (pt) REVERT: A 531 GLU cc_start: 0.8782 (mp0) cc_final: 0.8545 (mp0) REVERT: A 627 GLU cc_start: 0.7953 (mp0) cc_final: 0.7654 (mp0) REVERT: A 644 ARG cc_start: 0.8756 (ptt90) cc_final: 0.8309 (ptt-90) REVERT: A 645 PHE cc_start: 0.8532 (m-80) cc_final: 0.8077 (m-80) REVERT: A 713 MET cc_start: 0.7782 (tmm) cc_final: 0.7432 (tmm) REVERT: A 725 HIS cc_start: 0.7804 (t-90) cc_final: 0.7506 (t-90) REVERT: B 75 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7608 (t80) REVERT: B 140 PHE cc_start: 0.8602 (t80) cc_final: 0.8249 (t80) REVERT: B 157 ARG cc_start: 0.7474 (tpt-90) cc_final: 0.7118 (tpt-90) REVERT: B 186 MET cc_start: 0.8668 (tpp) cc_final: 0.8046 (ttp) REVERT: B 189 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8000 (mptt) REVERT: B 243 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8823 (tt) REVERT: B 297 PHE cc_start: 0.8859 (t80) cc_final: 0.8622 (t80) REVERT: B 300 MET cc_start: 0.8209 (tpp) cc_final: 0.7878 (tpp) REVERT: B 316 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7835 (tp30) REVERT: B 361 PHE cc_start: 0.8962 (t80) cc_final: 0.8524 (t80) REVERT: B 370 MET cc_start: 0.7502 (pmm) cc_final: 0.7269 (pmm) REVERT: B 441 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8910 (mp) outliers start: 51 outliers final: 40 residues processed: 312 average time/residue: 0.0679 time to fit residues: 31.4710 Evaluate side-chains 321 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 274 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 78 optimal weight: 0.2980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.142002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.118180 restraints weight = 16631.235| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.58 r_work: 0.3483 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10016 Z= 0.158 Angle : 0.740 11.578 13650 Z= 0.345 Chirality : 0.046 0.232 1613 Planarity : 0.004 0.053 1680 Dihedral : 5.505 57.069 1699 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.00 % Rotamer: Outliers : 4.43 % Allowed : 28.91 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.25), residues: 1179 helix: 0.75 (0.25), residues: 436 sheet: -1.70 (0.50), residues: 118 loop : -1.06 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.021 0.002 TYR B 158 PHE 0.035 0.002 PHE B 347 TRP 0.013 0.001 TRP B 476 HIS 0.013 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9991) covalent geometry : angle 0.73554 (13580) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.36836 ( 10) hydrogen bonds : bond 0.04403 ( 348) hydrogen bonds : angle 4.49845 ( 1032) link_BETA1-4 : bond 0.00363 ( 6) link_BETA1-4 : angle 1.57752 ( 18) link_NAG-ASN : bond 0.00193 ( 14) link_NAG-ASN : angle 1.27841 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8248 (t0) cc_final: 0.7923 (t0) REVERT: A 95 LEU cc_start: 0.9257 (tp) cc_final: 0.9018 (mm) REVERT: A 173 ASN cc_start: 0.8810 (m-40) cc_final: 0.8568 (m110) REVERT: A 183 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8382 (mmmm) REVERT: A 266 GLU cc_start: 0.8511 (tt0) cc_final: 0.8071 (tt0) REVERT: A 388 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 471 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8077 (mm110) REVERT: A 494 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8080 (mmmt) REVERT: A 531 GLU cc_start: 0.8789 (mp0) cc_final: 0.8566 (mp0) REVERT: A 627 GLU cc_start: 0.7960 (mp0) cc_final: 0.7662 (mp0) REVERT: A 644 ARG cc_start: 0.8766 (ptt90) cc_final: 0.8302 (ptt-90) REVERT: A 645 PHE cc_start: 0.8541 (m-80) cc_final: 0.8085 (m-80) REVERT: A 661 TRP cc_start: 0.8650 (t60) cc_final: 0.8244 (t60) REVERT: A 713 MET cc_start: 0.7786 (tmm) cc_final: 0.7427 (tmm) REVERT: A 725 HIS cc_start: 0.7866 (t-90) cc_final: 0.7650 (t-90) REVERT: B 75 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 140 PHE cc_start: 0.8599 (t80) cc_final: 0.8263 (t80) REVERT: B 186 MET cc_start: 0.8665 (tpp) cc_final: 0.8067 (ttp) REVERT: B 189 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8004 (mptt) REVERT: B 243 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8831 (tt) REVERT: B 297 PHE cc_start: 0.8819 (t80) cc_final: 0.8586 (t80) REVERT: B 300 MET cc_start: 0.8248 (tpp) cc_final: 0.7903 (tpp) REVERT: B 316 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: B 361 PHE cc_start: 0.8871 (t80) cc_final: 0.8439 (t80) REVERT: B 441 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8915 (mp) outliers start: 47 outliers final: 39 residues processed: 308 average time/residue: 0.0879 time to fit residues: 40.1626 Evaluate side-chains 320 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.145871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121192 restraints weight = 16654.827| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.75 r_work: 0.3522 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10016 Z= 0.124 Angle : 0.726 10.597 13650 Z= 0.337 Chirality : 0.045 0.233 1613 Planarity : 0.004 0.050 1680 Dihedral : 5.281 57.899 1699 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 4.14 % Allowed : 29.38 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.25), residues: 1179 helix: 0.74 (0.25), residues: 435 sheet: -1.68 (0.50), residues: 118 loop : -1.02 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.014 0.001 TYR B 182 PHE 0.033 0.001 PHE B 347 TRP 0.013 0.001 TRP B 477 HIS 0.017 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9991) covalent geometry : angle 0.72257 (13580) SS BOND : bond 0.00275 ( 5) SS BOND : angle 1.08287 ( 10) hydrogen bonds : bond 0.04102 ( 348) hydrogen bonds : angle 4.41683 ( 1032) link_BETA1-4 : bond 0.00419 ( 6) link_BETA1-4 : angle 1.48567 ( 18) link_NAG-ASN : bond 0.00187 ( 14) link_NAG-ASN : angle 1.20607 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2669.84 seconds wall clock time: 46 minutes 23.10 seconds (2783.10 seconds total)