Starting phenix.real_space_refine on Fri Sep 11 14:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c77_30294/09_2026/7c77_30294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c77_30294/09_2026/7c77_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_30294/09_2026/7c77_30294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c77_30294/09_2026/7c77_30294.map" model { file = "/net/cci-nas-00/data/ceres_data/7c77_30294/09_2026/7c77_30294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c77_30294/09_2026/7c77_30294.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7c77_30294/09_2026/7c77_30294.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c77_30294/09_2026/7c77_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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: 0.89 Conformation dependent library (CDL) restraints added in 338.5 milliseconds 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: 0.27 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: 1.67 Time building geometry restraints manager: 1.17 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 - 16.91: 4881 16.91 - 33.82: 703 33.82 - 50.74: 161 50.74 - 67.65: 24 67.65 - 84.56: 15 Dihedral angle restraints: 5784 sinusoidal: 2312 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 5781 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.920 Find NCS groups from input model: 0.060 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 16.457 84.562 3527 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 are 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/Z covalent geometry : bond 0.00332 / 0.18 ( 9991) covalent geometry : angle 0.66767 / 0.34 (13580) SS BOND : bond 0.00124 / 0.06 ( 5) SS BOND : angle 0.41810 / 0.24 ( 10) hydrogen bonds : bond 0.15399 / 10.17 ( 348) hydrogen bonds : angle 5.70740 / 3.89 ( 1032) link_BETA1-4 : bond 0.00333 / 0.17 ( 6) link_BETA1-4 : angle 1.26186 / 0.82 ( 18) link_NAG-ASN : bond 0.00214 / 0.15 ( 14) link_NAG-ASN : angle 0.98377 / 0.75 ( 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 : 0.377 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: 0.0815 time to fit residues: 41.7264 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 : 0.388 ------------------------------------------------------------------------------- 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... A 62 ASN A 110 ASN A 182 ASN A 344 HIS A 418 ASN A 619 GLN B 412 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.145185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.121683 restraints weight = 17009.578| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.74 r_work: 0.3540 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10016 Z= 0.250 Angle : 0.755 9.984 13650 Z= 0.366 Chirality : 0.048 0.245 1613 Planarity : 0.005 0.047 1680 Dihedral : 5.138 55.364 1291 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.52 % Allowed : 19.59 % Favored : 75.89 % 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 are not related in a simple way. whole: -1.49 (0.24), residues: 1179 helix: 0.08 (0.25), residues: 445 sheet: -1.64 (0.48), residues: 116 loop : -1.67 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 644 TYR 0.018 0.002 TYR A 303 PHE 0.025 0.002 PHE B 347 TRP 0.014 0.001 TRP B 476 HIS 0.008 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 ( 9991) covalent geometry : angle 0.74958 / 0.36 (13580) SS BOND : bond 0.02308 / 1.21 ( 5) SS BOND : angle 1.02354 / 0.62 ( 10) hydrogen bonds : bond 0.04869 / 3.19 ( 348) hydrogen bonds : angle 4.67781 / 3.16 ( 1032) link_BETA1-4 : bond 0.00272 / 0.13 ( 6) link_BETA1-4 : angle 1.60838 / 1.10 ( 18) link_NAG-ASN : bond 0.00347 / 0.24 ( 14) link_NAG-ASN : angle 1.45871 / 1.05 ( 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 347 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 299 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8212 (t0) cc_final: 0.7816 (t0) REVERT: A 183 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8132 (mtmm) REVERT: A 330 LEU cc_start: 0.9210 (mm) cc_final: 0.8991 (mp) REVERT: A 364 ASP cc_start: 0.7944 (m-30) cc_final: 0.7690 (m-30) REVERT: A 494 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8218 (mmmt) REVERT: A 545 ARG cc_start: 0.8480 (tpm170) cc_final: 0.8055 (tpm170) REVERT: A 626 VAL cc_start: 0.9009 (t) cc_final: 0.8799 (t) REVERT: A 627 GLU cc_start: 0.8150 (mp0) cc_final: 0.7896 (mp0) REVERT: A 644 ARG cc_start: 0.8743 (ptt90) cc_final: 0.8216 (ptt-90) REVERT: B 106 ASP cc_start: 0.8099 (t70) cc_final: 0.7815 (t0) REVERT: B 189 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8019 (mptt) REVERT: B 297 PHE cc_start: 0.8522 (t80) cc_final: 0.8273 (t80) REVERT: B 370 MET cc_start: 0.7582 (pmm) cc_final: 0.7197 (pmm) REVERT: B 441 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8889 (mp) REVERT: B 478 GLN cc_start: 0.8404 (tt0) cc_final: 0.7965 (tt0) outliers start: 48 outliers final: 35 residues processed: 323 average time/residue: 0.0832 time to fit residues: 39.5733 Evaluate side-chains 306 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 344 HIS A 610 GLN B 195 HIS B 229 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126175 restraints weight = 16332.608| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.67 r_work: 0.3584 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2247 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= 0.122 Angle : 0.651 12.245 13650 Z= 0.308 Chirality : 0.044 0.246 1613 Planarity : 0.004 0.049 1680 Dihedral : 4.775 55.350 1288 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.39 % Allowed : 23.45 % Favored : 73.16 % 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 are not related in a simple way. whole: -1.18 (0.24), residues: 1179 helix: 0.32 (0.25), residues: 444 sheet: -1.47 (0.49), residues: 116 loop : -1.48 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.019 0.001 TYR B 158 PHE 0.037 0.001 PHE B 347 TRP 0.008 0.001 TRP B 476 HIS 0.011 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9991) covalent geometry : angle 0.64543 / 0.31 (13580) SS BOND : bond 0.00531 / 0.28 ( 5) SS BOND : angle 1.85253 / 1.09 ( 10) hydrogen bonds : bond 0.04143 / 2.74 ( 348) hydrogen bonds : angle 4.41098 / 2.99 ( 1032) link_BETA1-4 : bond 0.00432 / 0.23 ( 6) link_BETA1-4 : angle 1.36702 / 0.96 ( 18) link_NAG-ASN : bond 0.00174 / 0.13 ( 14) link_NAG-ASN : angle 1.12887 / 0.81 ( 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 331 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8033 (t0) cc_final: 0.7683 (t0) REVERT: A 103 LYS cc_start: 0.8025 (ptpt) cc_final: 0.7716 (mmtt) REVERT: A 132 MET cc_start: 0.7351 (tmm) cc_final: 0.7080 (tmm) REVERT: A 183 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8217 (mtmm) REVERT: A 493 LEU cc_start: 0.9175 (tp) cc_final: 0.8847 (tp) REVERT: A 494 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8050 (mmmt) REVERT: A 545 ARG cc_start: 0.8442 (tpm170) cc_final: 0.8105 (tpm170) REVERT: A 621 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7805 (m110) REVERT: A 626 VAL cc_start: 0.8972 (t) cc_final: 0.8743 (t) REVERT: A 627 GLU cc_start: 0.8133 (mp0) cc_final: 0.7822 (mp0) REVERT: A 644 ARG cc_start: 0.8752 (ptt90) cc_final: 0.8198 (ptt-90) REVERT: B 186 MET cc_start: 0.8792 (tpp) cc_final: 0.8146 (ttp) REVERT: B 189 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7945 (mptt) REVERT: B 244 ASN cc_start: 0.8782 (m110) cc_final: 0.8457 (m110) REVERT: B 297 PHE cc_start: 0.8541 (t80) cc_final: 0.8289 (t80) REVERT: B 370 MET cc_start: 0.7467 (pmm) cc_final: 0.7109 (pmm) REVERT: B 441 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8872 (mp) REVERT: B 478 GLN cc_start: 0.8281 (tt0) cc_final: 0.7881 (tt0) outliers start: 36 outliers final: 20 residues processed: 315 average time/residue: 0.0872 time to fit residues: 40.4186 Evaluate side-chains 303 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 261 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 621 ASN Chi-restraints excluded: chain A residue 651 THR 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 188 GLN Chi-restraints excluded: chain B residue 230 LEU 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 375 LEU Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 441 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: 0.9990 chunk 82 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 HIS A 646 ASN B 83 GLN B 195 HIS B 284 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.145895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.122161 restraints weight = 16985.037| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.75 r_work: 0.3544 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10016 Z= 0.124 Angle : 0.633 11.032 13650 Z= 0.299 Chirality : 0.044 0.251 1613 Planarity : 0.004 0.051 1680 Dihedral : 4.546 56.315 1285 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 5.46 % Allowed : 23.26 % Favored : 71.28 % 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 are not related in a simple way. whole: -0.93 (0.25), residues: 1179 helix: 0.57 (0.25), residues: 444 sheet: -1.42 (0.50), residues: 116 loop : -1.34 (0.25), 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 0.036 0.001 PHE B 347 TRP 0.010 0.001 TRP B 476 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 9991) covalent geometry : angle 0.62823 / 0.30 (13580) SS BOND : bond 0.00408 / 0.21 ( 5) SS BOND : angle 1.25176 / 0.74 ( 10) hydrogen bonds : bond 0.03940 / 2.63 ( 348) hydrogen bonds : angle 4.29355 / 2.91 ( 1032) link_BETA1-4 : bond 0.00373 / 0.19 ( 6) link_BETA1-4 : angle 1.41039 / 1.00 ( 18) link_NAG-ASN : bond 0.00157 / 0.12 ( 14) link_NAG-ASN : angle 1.14551 / 0.81 ( 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 347 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 289 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8010 (t0) cc_final: 0.7692 (t0) REVERT: A 173 ASN cc_start: 0.8764 (m-40) cc_final: 0.8453 (m110) REVERT: A 183 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8350 (mmmm) REVERT: A 388 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 464 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8941 (mt) REVERT: A 493 LEU cc_start: 0.9107 (tp) cc_final: 0.8874 (tp) REVERT: A 494 LYS cc_start: 0.8640 (mmmm) cc_final: 0.7971 (mmmt) REVERT: A 519 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8166 (pt) REVERT: A 545 ARG cc_start: 0.8545 (tpm170) cc_final: 0.8198 (tpm170) REVERT: A 644 ARG cc_start: 0.8734 (ptt90) cc_final: 0.7890 (ptt-90) REVERT: A 645 PHE cc_start: 0.8609 (m-80) cc_final: 0.7884 (m-80) REVERT: B 75 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 129 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8277 (pp) REVERT: B 186 MET cc_start: 0.8611 (tpp) cc_final: 0.8002 (ttp) REVERT: B 189 LYS cc_start: 0.8565 (ttmm) cc_final: 0.7971 (mptt) REVERT: B 297 PHE cc_start: 0.8410 (t80) cc_final: 0.8159 (t80) REVERT: B 441 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8891 (mp) REVERT: B 478 GLN cc_start: 0.8233 (tt0) cc_final: 0.7762 (tt0) outliers start: 58 outliers final: 39 residues processed: 319 average time/residue: 0.0846 time to fit residues: 39.7649 Evaluate side-chains 324 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 275 THR Chi-restraints excluded: chain A residue 301 LEU 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 472 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 571 GLU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 611 THR 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 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 106 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 304 LEU 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 Chi-restraints excluded: chain B residue 505 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 97 optimal weight: 0.0870 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 344 HIS ** 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 = 0.3944 r_free = 0.3944 target = 0.145447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121826 restraints weight = 16912.904| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.73 r_work: 0.3519 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10016 Z= 0.142 Angle : 0.645 10.811 13650 Z= 0.307 Chirality : 0.044 0.249 1613 Planarity : 0.004 0.051 1680 Dihedral : 4.615 57.352 1285 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 5.46 % Allowed : 24.95 % 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 are not related in a simple way. whole: -0.83 (0.25), residues: 1179 helix: 0.68 (0.25), residues: 442 sheet: -1.48 (0.50), residues: 118 loop : -1.28 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.019 0.001 TYR B 158 PHE 0.037 0.001 PHE B 347 TRP 0.011 0.001 TRP B 476 HIS 0.006 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 9991) covalent geometry : angle 0.63777 / 0.30 (13580) SS BOND : bond 0.00344 / 0.18 ( 5) SS BOND : angle 2.69021 / 1.15 ( 10) hydrogen bonds : bond 0.04007 / 2.65 ( 348) hydrogen bonds : angle 4.34336 / 2.95 ( 1032) link_BETA1-4 : bond 0.00335 / 0.18 ( 6) link_BETA1-4 : angle 1.43135 / 1.00 ( 18) link_NAG-ASN : bond 0.00154 / 0.11 ( 14) link_NAG-ASN : angle 1.13434 / 0.80 ( 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 340 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8076 (t0) cc_final: 0.7762 (t0) REVERT: A 132 MET cc_start: 0.7297 (tmm) cc_final: 0.7005 (tmm) REVERT: A 173 ASN cc_start: 0.8751 (m-40) cc_final: 0.8439 (m110) REVERT: A 183 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8396 (mmmm) REVERT: A 388 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8367 (p) REVERT: A 464 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8961 (mt) REVERT: A 471 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8053 (mm110) REVERT: A 493 LEU cc_start: 0.9119 (tp) cc_final: 0.8881 (tp) REVERT: A 494 LYS cc_start: 0.8653 (mmmm) cc_final: 0.7953 (mmmt) REVERT: A 519 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8107 (pt) REVERT: A 627 GLU cc_start: 0.8104 (mp0) cc_final: 0.7851 (mp0) REVERT: A 644 ARG cc_start: 0.8752 (ptt90) cc_final: 0.8336 (ptt-90) REVERT: A 645 PHE cc_start: 0.8537 (m-80) cc_final: 0.8041 (m-80) REVERT: B 75 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 139 MET cc_start: 0.8991 (mmm) cc_final: 0.8218 (mmm) REVERT: B 179 MET cc_start: 0.9091 (tpp) cc_final: 0.8598 (tpp) REVERT: B 186 MET cc_start: 0.8619 (tpp) cc_final: 0.8014 (ttp) REVERT: B 189 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7954 (mptt) REVERT: B 297 PHE cc_start: 0.8547 (t80) cc_final: 0.8259 (t80) REVERT: B 441 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8888 (mp) REVERT: B 478 GLN cc_start: 0.8245 (tt0) cc_final: 0.7797 (tt0) outliers start: 58 outliers final: 36 residues processed: 314 average time/residue: 0.0803 time to fit residues: 37.4990 Evaluate side-chains 322 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 301 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 464 LEU Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 533 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 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 106 ASP 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: 1.9990 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 517 ASN ** A 646 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115701 restraints weight = 17040.900| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.67 r_work: 0.3443 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10016 Z= 0.221 Angle : 0.729 10.638 13650 Z= 0.350 Chirality : 0.047 0.251 1613 Planarity : 0.005 0.050 1680 Dihedral : 4.801 58.177 1281 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 6.31 % Allowed : 24.86 % Favored : 68.83 % 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 are not related in a simple way. whole: -0.72 (0.25), residues: 1179 helix: 0.79 (0.26), residues: 431 sheet: -1.60 (0.50), residues: 118 loop : -1.16 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 545 TYR 0.020 0.002 TYR B 158 PHE 0.037 0.002 PHE B 347 TRP 0.018 0.001 TRP B 476 HIS 0.005 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 9991) covalent geometry : angle 0.72167 / 0.35 (13580) SS BOND : bond 0.00420 / 0.23 ( 5) SS BOND : angle 1.98332 / 0.95 ( 10) hydrogen bonds : bond 0.04767 / 3.12 ( 348) hydrogen bonds : angle 4.60199 / 3.13 ( 1032) link_BETA1-4 : bond 0.00344 / 0.18 ( 6) link_BETA1-4 : angle 1.77217 / 1.19 ( 18) link_NAG-ASN : bond 0.00301 / 0.20 ( 14) link_NAG-ASN : angle 1.36094 / 0.92 ( 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 343 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8210 (t0) cc_final: 0.7844 (t0) REVERT: A 183 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8400 (mmmm) REVERT: A 246 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8900 (tt) REVERT: A 266 GLU cc_start: 0.8486 (tt0) cc_final: 0.8075 (tt0) REVERT: A 388 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 464 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9071 (mt) REVERT: A 471 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8075 (mm110) REVERT: A 514 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8444 (pt) REVERT: A 519 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8318 (pt) REVERT: A 531 GLU cc_start: 0.8804 (mp0) cc_final: 0.8585 (mp0) REVERT: B 106 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7597 (t0) REVERT: B 186 MET cc_start: 0.8704 (tpp) cc_final: 0.8035 (ttp) REVERT: B 189 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7929 (mptt) REVERT: B 297 PHE cc_start: 0.8752 (t80) cc_final: 0.8540 (t80) REVERT: B 316 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: B 370 MET cc_start: 0.7466 (pmm) cc_final: 0.7231 (pmm) REVERT: B 441 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8870 (mp) outliers start: 67 outliers final: 46 residues processed: 316 average time/residue: 0.0781 time to fit residues: 37.0934 Evaluate side-chains 314 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 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 464 LEU 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 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 88 LEU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 130 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 267 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 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 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 Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.138881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115067 restraints weight = 17133.906| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.66 r_work: 0.3456 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10016 Z= 0.194 Angle : 0.723 10.901 13650 Z= 0.343 Chirality : 0.047 0.242 1613 Planarity : 0.004 0.049 1680 Dihedral : 4.789 56.749 1281 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 5.84 % Allowed : 27.21 % 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 are not related in a simple way. whole: -0.67 (0.25), residues: 1179 helix: 0.85 (0.25), residues: 431 sheet: -1.68 (0.50), residues: 118 loop : -1.11 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.019 0.002 TYR B 158 PHE 0.036 0.002 PHE B 347 TRP 0.015 0.001 TRP B 476 HIS 0.006 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 9991) covalent geometry : angle 0.71780 / 0.34 (13580) SS BOND : bond 0.00417 / 0.23 ( 5) SS BOND : angle 1.50218 / 0.76 ( 10) hydrogen bonds : bond 0.04598 / 3.03 ( 348) hydrogen bonds : angle 4.57498 / 3.10 ( 1032) link_BETA1-4 : bond 0.00384 / 0.20 ( 6) link_BETA1-4 : angle 1.64535 / 1.09 ( 18) link_NAG-ASN : bond 0.00223 / 0.15 ( 14) link_NAG-ASN : angle 1.28262 / 0.86 ( 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 335 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8252 (t0) cc_final: 0.7897 (t0) REVERT: A 95 LEU cc_start: 0.9255 (tp) cc_final: 0.8994 (mm) REVERT: A 132 MET cc_start: 0.7380 (tmm) cc_final: 0.7098 (tmm) REVERT: A 183 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8359 (mmmm) REVERT: A 192 LEU cc_start: 0.9063 (mm) cc_final: 0.8853 (mm) REVERT: A 266 GLU cc_start: 0.8472 (tt0) cc_final: 0.7986 (tt0) REVERT: A 388 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8481 (p) REVERT: A 471 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8028 (mm110) REVERT: A 514 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8479 (pt) REVERT: A 531 GLU cc_start: 0.8828 (mp0) cc_final: 0.8610 (mp0) REVERT: A 627 GLU cc_start: 0.8071 (mp0) cc_final: 0.7753 (mp0) REVERT: A 645 PHE cc_start: 0.8527 (m-80) cc_final: 0.8287 (m-80) REVERT: B 75 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7977 (t80) REVERT: B 106 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7427 (t0) REVERT: B 139 MET cc_start: 0.9074 (mmm) cc_final: 0.8137 (mmm) REVERT: B 157 ARG cc_start: 0.7578 (tpt-90) cc_final: 0.7215 (tpt-90) REVERT: B 179 MET cc_start: 0.9085 (tpp) cc_final: 0.8595 (tpp) REVERT: B 186 MET cc_start: 0.8690 (tpp) cc_final: 0.8016 (ttp) REVERT: B 189 LYS cc_start: 0.8499 (ttmm) cc_final: 0.7969 (mptt) REVERT: B 243 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8881 (tt) REVERT: B 316 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: B 441 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8907 (mp) outliers start: 62 outliers final: 38 residues processed: 311 average time/residue: 0.0731 time to fit residues: 34.4256 Evaluate side-chains 308 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 514 LEU 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 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 106 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 173 ASN A 309 ASN A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 195 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117396 restraints weight = 16952.722| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.71 r_work: 0.3493 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 0.041 10016 Z= 0.131 Angle : 0.692 9.740 13650 Z= 0.324 Chirality : 0.045 0.241 1613 Planarity : 0.004 0.050 1680 Dihedral : 4.591 56.857 1281 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 4.52 % Allowed : 28.44 % Favored : 67.04 % 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 are not related in a simple way. whole: -0.55 (0.25), residues: 1179 helix: 0.94 (0.26), residues: 430 sheet: -1.68 (0.50), residues: 118 loop : -1.02 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 490 TYR 0.018 0.001 TYR B 158 PHE 0.036 0.002 PHE B 347 TRP 0.011 0.001 TRP B 476 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9991) covalent geometry : angle 0.68805 / 0.32 (13580) SS BOND : bond 0.00323 / 0.17 ( 5) SS BOND : angle 1.18130 / 0.61 ( 10) hydrogen bonds : bond 0.04188 / 2.78 ( 348) hydrogen bonds : angle 4.46301 / 3.03 ( 1032) link_BETA1-4 : bond 0.00392 / 0.21 ( 6) link_BETA1-4 : angle 1.46000 / 1.00 ( 18) link_NAG-ASN : bond 0.00134 / 0.09 ( 14) link_NAG-ASN : angle 1.18830 / 0.81 ( 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 337 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 289 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8228 (t0) cc_final: 0.7880 (t0) REVERT: A 95 LEU cc_start: 0.9262 (tp) cc_final: 0.9006 (mm) REVERT: A 132 MET cc_start: 0.7142 (tmm) cc_final: 0.6919 (tmm) REVERT: A 183 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8348 (mmmm) REVERT: A 266 GLU cc_start: 0.8464 (tt0) cc_final: 0.8070 (tt0) REVERT: A 388 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 433 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: A 439 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8730 (mt) REVERT: A 471 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7871 (mm110) REVERT: A 494 LYS cc_start: 0.8692 (mmmm) cc_final: 0.7931 (mmmt) REVERT: A 514 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8392 (pt) REVERT: A 531 GLU cc_start: 0.8746 (mp0) cc_final: 0.8540 (mp0) REVERT: A 627 GLU cc_start: 0.7938 (mp0) cc_final: 0.7649 (mp0) REVERT: A 645 PHE cc_start: 0.8489 (m-80) cc_final: 0.8028 (m-80) REVERT: A 661 TRP cc_start: 0.8643 (t60) cc_final: 0.8252 (t60) REVERT: B 50 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7921 (ttp80) REVERT: B 75 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.7593 (t80) REVERT: B 186 MET cc_start: 0.8731 (tpp) cc_final: 0.8005 (ttp) REVERT: B 189 LYS cc_start: 0.8511 (ttmm) cc_final: 0.7986 (mptt) REVERT: B 243 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8876 (tt) outliers start: 48 outliers final: 32 residues processed: 316 average time/residue: 0.0808 time to fit residues: 38.0859 Evaluate side-chains 320 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 388 SER Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 514 LEU 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 707 PHE 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 106 ASP 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 243 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 304 LEU 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 378 LEU Chi-restraints excluded: chain B residue 429 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: 5.9990 chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS ** 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 = 0.3908 r_free = 0.3908 target = 0.141433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117304 restraints weight = 16719.520| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.64 r_work: 0.3474 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10016 Z= 0.156 Angle : 0.718 9.452 13650 Z= 0.340 Chirality : 0.046 0.245 1613 Planarity : 0.004 0.051 1680 Dihedral : 4.649 56.031 1281 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 4.80 % Allowed : 28.91 % Favored : 66.29 % 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 are not related in a simple way. whole: -0.57 (0.25), residues: 1179 helix: 0.92 (0.25), residues: 430 sheet: -1.71 (0.50), residues: 118 loop : -1.01 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.018 0.002 TYR B 158 PHE 0.036 0.002 PHE B 347 TRP 0.014 0.001 TRP B 476 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9991) covalent geometry : angle 0.71322 / 0.34 (13580) SS BOND : bond 0.00338 / 0.18 ( 5) SS BOND : angle 1.17255 / 0.63 ( 10) hydrogen bonds : bond 0.04313 / 2.86 ( 348) hydrogen bonds : angle 4.49819 / 3.06 ( 1032) link_BETA1-4 : bond 0.00358 / 0.19 ( 6) link_BETA1-4 : angle 1.56681 / 1.05 ( 18) link_NAG-ASN : bond 0.00186 / 0.13 ( 14) link_NAG-ASN : angle 1.24696 / 0.85 ( 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 338 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8259 (t0) cc_final: 0.7865 (t0) REVERT: A 95 LEU cc_start: 0.9274 (tp) cc_final: 0.9017 (mm) REVERT: A 132 MET cc_start: 0.7176 (tmm) cc_final: 0.6938 (tmm) REVERT: A 183 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8368 (mmmm) REVERT: A 266 GLU cc_start: 0.8504 (tt0) cc_final: 0.8096 (tt0) REVERT: A 388 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 433 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8352 (tp40) REVERT: A 471 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7991 (mm110) REVERT: A 494 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8021 (mmmt) REVERT: A 514 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8433 (pt) REVERT: A 531 GLU cc_start: 0.8781 (mp0) cc_final: 0.8551 (mp0) REVERT: A 627 GLU cc_start: 0.7939 (mp0) cc_final: 0.7649 (mp0) REVERT: A 645 PHE cc_start: 0.8546 (m-80) cc_final: 0.8029 (m-80) REVERT: A 661 TRP cc_start: 0.8627 (t60) cc_final: 0.8256 (t60) REVERT: B 50 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7944 (ttp80) REVERT: B 75 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 157 ARG cc_start: 0.7533 (tpt-90) cc_final: 0.7268 (tpt-90) REVERT: B 179 MET cc_start: 0.9103 (tpp) cc_final: 0.8692 (tpp) REVERT: B 186 MET cc_start: 0.8720 (tpp) cc_final: 0.7971 (ttp) REVERT: B 189 LYS cc_start: 0.8510 (ttmm) cc_final: 0.7980 (mptt) REVERT: B 243 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8854 (tt) REVERT: B 316 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: B 467 GLN cc_start: 0.7617 (mt0) cc_final: 0.7390 (mt0) outliers start: 51 outliers final: 40 residues processed: 321 average time/residue: 0.0825 time to fit residues: 39.4245 Evaluate side-chains 323 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 433 GLN Chi-restraints excluded: chain A residue 439 LEU 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 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 571 GLU 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 106 ASP 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 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 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: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 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 = 0.3857 r_free = 0.3857 target = 0.138538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115050 restraints weight = 17061.446| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.64 r_work: 0.3447 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10016 Z= 0.194 Angle : 0.757 9.877 13650 Z= 0.359 Chirality : 0.047 0.243 1613 Planarity : 0.004 0.056 1680 Dihedral : 4.795 53.985 1281 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 4.52 % Allowed : 28.91 % Favored : 66.57 % 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 are not related in a simple way. whole: -0.69 (0.25), residues: 1179 helix: 0.81 (0.25), residues: 431 sheet: -1.78 (0.50), residues: 118 loop : -1.09 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.018 0.002 TYR B 248 PHE 0.036 0.002 PHE B 347 TRP 0.015 0.001 TRP B 476 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 9991) covalent geometry : angle 0.75171 / 0.36 (13580) SS BOND : bond 0.00389 / 0.22 ( 5) SS BOND : angle 1.51697 / 0.85 ( 10) hydrogen bonds : bond 0.04598 / 3.06 ( 348) hydrogen bonds : angle 4.58630 / 3.11 ( 1032) link_BETA1-4 : bond 0.00376 / 0.19 ( 6) link_BETA1-4 : angle 1.69103 / 1.11 ( 18) link_NAG-ASN : bond 0.00256 / 0.17 ( 14) link_NAG-ASN : angle 1.35482 / 0.90 ( 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 318 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8207 (t0) cc_final: 0.7867 (t0) REVERT: A 95 LEU cc_start: 0.9299 (tp) cc_final: 0.9034 (mm) REVERT: A 132 MET cc_start: 0.7236 (tmm) cc_final: 0.6945 (tmm) REVERT: A 173 ASN cc_start: 0.8964 (m-40) cc_final: 0.8752 (m110) REVERT: A 183 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8378 (mmmm) REVERT: A 266 GLU cc_start: 0.8479 (tt0) cc_final: 0.8013 (tt0) REVERT: A 388 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 433 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8397 (tp40) REVERT: A 471 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8011 (mm110) REVERT: A 514 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8491 (pt) REVERT: A 531 GLU cc_start: 0.8837 (mp0) cc_final: 0.8613 (mp0) REVERT: A 627 GLU cc_start: 0.7965 (mp0) cc_final: 0.7648 (mp0) REVERT: A 645 PHE cc_start: 0.8592 (m-80) cc_final: 0.8322 (m-80) REVERT: B 50 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8111 (ttp80) REVERT: B 179 MET cc_start: 0.9103 (tpp) cc_final: 0.8718 (tpp) REVERT: B 186 MET cc_start: 0.8677 (tpp) cc_final: 0.7988 (ttp) REVERT: B 189 LYS cc_start: 0.8513 (ttmm) cc_final: 0.7987 (mptt) REVERT: B 243 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8863 (tt) outliers start: 48 outliers final: 39 residues processed: 302 average time/residue: 0.0834 time to fit residues: 37.3516 Evaluate side-chains 312 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 433 GLN 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 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 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 106 ASP 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 243 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 429 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: 8.9990 chunk 9 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 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 = 0.3912 r_free = 0.3912 target = 0.141715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.117320 restraints weight = 16632.636| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.65 r_work: 0.3472 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10016 Z= 0.149 Angle : 0.744 10.567 13650 Z= 0.348 Chirality : 0.046 0.243 1613 Planarity : 0.004 0.064 1680 Dihedral : 4.685 54.022 1281 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 4.33 % Allowed : 29.47 % Favored : 66.20 % 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 are not related in a simple way. whole: -0.64 (0.25), residues: 1179 helix: 0.82 (0.25), residues: 430 sheet: -1.79 (0.50), residues: 118 loop : -1.02 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.019 0.001 TYR B 158 PHE 0.035 0.002 PHE B 347 TRP 0.012 0.001 TRP B 137 HIS 0.008 0.001 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9991) covalent geometry : angle 0.73916 / 0.35 (13580) SS BOND : bond 0.00286 / 0.15 ( 5) SS BOND : angle 1.28332 / 0.71 ( 10) hydrogen bonds : bond 0.04324 / 2.88 ( 348) hydrogen bonds : angle 4.51993 / 3.07 ( 1032) link_BETA1-4 : bond 0.00386 / 0.20 ( 6) link_BETA1-4 : angle 1.54727 / 1.04 ( 18) link_NAG-ASN : bond 0.00154 / 0.11 ( 14) link_NAG-ASN : angle 1.31494 / 0.92 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.31 seconds wall clock time: 49 minutes 31.54 seconds (2971.54 seconds total)