Starting phenix.real_space_refine on Mon Jul 28 00:12:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c77_30294/07_2025/7c77_30294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c77_30294/07_2025/7c77_30294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c77_30294/07_2025/7c77_30294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c77_30294/07_2025/7c77_30294.map" model { file = "/net/cci-nas-00/data/ceres_data/7c77_30294/07_2025/7c77_30294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c77_30294/07_2025/7c77_30294.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5616 Classifications: {'peptide': 700} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 670} Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3869 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 21, 'TRANS': 461} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.61, per 1000 atoms: 0.57 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 3.07 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3018 1.34 - 1.46: 1809 1.46 - 1.58: 5107 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 9991 Sorted by residual: bond pdb=" N ALA B 506 " pdb=" CA ALA B 506 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.19e-02 7.06e+03 6.48e+00 bond pdb=" CA ALA B 506 " pdb=" C ALA B 506 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.27e-02 6.20e+03 4.33e+00 bond pdb=" C ALA B 506 " pdb=" O ALA B 506 " ideal model delta sigma weight residual 1.236 1.257 -0.021 1.15e-02 7.56e+03 3.21e+00 bond pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.01e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.48e+00 ... (remaining 9986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 12932 1.41 - 2.81: 526 2.81 - 4.22: 83 4.22 - 5.62: 31 5.62 - 7.03: 8 Bond angle restraints: 13580 Sorted by residual: angle pdb=" C SER B 510 " pdb=" N TYR B 511 " pdb=" CA TYR B 511 " ideal model delta sigma weight residual 120.54 124.87 -4.33 1.35e+00 5.49e-01 1.03e+01 angle pdb=" CA GLY B 266 " pdb=" C GLY B 266 " pdb=" N ILE B 267 " ideal model delta sigma weight residual 114.23 116.75 -2.52 8.80e-01 1.29e+00 8.17e+00 angle pdb=" CA SER B 510 " pdb=" C SER B 510 " pdb=" N TYR B 511 " ideal model delta sigma weight residual 117.39 114.08 3.31 1.24e+00 6.50e-01 7.14e+00 angle pdb=" C TRP A 547 " pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.69e+00 angle pdb=" CA VAL B 275 " pdb=" C VAL B 275 " pdb=" N LEU B 276 " ideal model delta sigma weight residual 116.60 120.16 -3.56 1.45e+00 4.76e-01 6.04e+00 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 5534 21.71 - 43.42: 568 43.42 - 65.13: 74 65.13 - 86.85: 22 86.85 - 108.56: 4 Dihedral angle restraints: 6202 sinusoidal: 2730 harmonic: 3472 Sorted by residual: dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 38 " pdb=" CB CYS A 38 " ideal model delta sinusoidal sigma weight residual -86.00 -24.67 -61.33 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual -86.00 -51.65 -34.35 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CB CYS B 260 " pdb=" SG CYS B 260 " pdb=" SG CYS B 368 " pdb=" CB CYS B 368 " ideal model delta sinusoidal sigma weight residual 93.00 125.81 -32.81 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 6199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1364 0.055 - 0.109: 226 0.109 - 0.163: 21 0.163 - 0.218: 1 0.218 - 0.272: 1 Chirality restraints: 1613 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C2 NAG A1002 " pdb=" C1 NAG A1002 " pdb=" C3 NAG A1002 " pdb=" N2 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1610 not shown) Planarity restraints: 1694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 207 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO B 208 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 506 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C ALA B 506 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA B 506 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 507 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 118 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 119 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.025 5.00e-02 4.00e+02 ... (remaining 1691 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 969 2.75 - 3.29: 9757 3.29 - 3.82: 16278 3.82 - 4.36: 18331 4.36 - 4.90: 31933 Nonbonded interactions: 77268 Sorted by model distance: nonbonded pdb=" OH TYR B 248 " pdb=" O THR B 274 " model vdw 2.209 3.040 nonbonded pdb=" O SER A 373 " pdb=" OG SER A 404 " model vdw 2.269 3.040 nonbonded pdb=" O SER A 475 " pdb=" OG SER A 475 " model vdw 2.292 3.040 nonbonded pdb=" O HIS B 229 " pdb=" OG SER B 383 " model vdw 2.292 3.040 nonbonded pdb=" O ALA B 222 " pdb=" OG SER B 390 " model vdw 2.304 3.040 ... (remaining 77263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.620 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10016 Z= 0.176 Angle : 0.670 7.030 13650 Z= 0.341 Chirality : 0.041 0.272 1613 Planarity : 0.004 0.065 1680 Dihedral : 16.649 108.557 3945 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (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 TRP 0.007 0.001 TRP A 547 HIS 0.005 0.000 HIS B 475 PHE 0.016 0.001 PHE A 692 TYR 0.017 0.001 TYR B 511 ARG 0.007 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 14) link_NAG-ASN : angle 0.98377 ( 42) link_BETA1-4 : bond 0.00333 ( 6) link_BETA1-4 : angle 1.26186 ( 18) hydrogen bonds : bond 0.15399 ( 348) hydrogen bonds : angle 5.70740 ( 1032) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.41810 ( 10) covalent geometry : bond 0.00332 ( 9991) covalent geometry : angle 0.66767 (13580) *********************** 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 : 1.161 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: 0.1945 time to fit residues: 97.7257 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 : 1.136 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 110 ASN A 344 HIS A 418 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN B 412 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.147262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123292 restraints weight = 16459.231| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.66 r_work: 0.3552 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10016 Z= 0.243 Angle : 0.746 9.391 13650 Z= 0.360 Chirality : 0.048 0.247 1613 Planarity : 0.005 0.047 1680 Dihedral : 7.939 70.111 1709 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.52 % Allowed : 19.30 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.24), residues: 1179 helix: 0.05 (0.25), residues: 445 sheet: -1.64 (0.48), residues: 116 loop : -1.71 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 476 HIS 0.008 0.001 HIS B 195 PHE 0.025 0.002 PHE B 347 TYR 0.017 0.002 TYR A 327 ARG 0.006 0.001 ARG B 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 14) link_NAG-ASN : angle 1.38029 ( 42) link_BETA1-4 : bond 0.00552 ( 6) link_BETA1-4 : angle 1.91583 ( 18) hydrogen bonds : bond 0.04926 ( 348) hydrogen bonds : angle 4.66692 ( 1032) SS BOND : bond 0.00815 ( 5) SS BOND : angle 0.81756 ( 10) covalent geometry : bond 0.00557 ( 9991) covalent geometry : angle 0.74075 (13580) *********************** 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 345 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 297 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8183 (t0) cc_final: 0.7813 (t0) REVERT: A 176 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6858 (mp0) REVERT: A 183 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8133 (mtmm) REVERT: A 330 LEU cc_start: 0.9207 (mm) cc_final: 0.8981 (mp) REVERT: A 364 ASP cc_start: 0.7949 (m-30) cc_final: 0.7726 (m-30) REVERT: A 494 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8283 (mmmt) REVERT: A 545 ARG cc_start: 0.8489 (tpm170) cc_final: 0.8063 (tpm170) REVERT: A 626 VAL cc_start: 0.9005 (t) cc_final: 0.8795 (t) REVERT: A 627 GLU cc_start: 0.8136 (mp0) cc_final: 0.7881 (mp0) REVERT: A 644 ARG cc_start: 0.8754 (ptt90) cc_final: 0.8240 (ptt-90) REVERT: B 106 ASP cc_start: 0.8069 (t70) cc_final: 0.7786 (t0) REVERT: B 189 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8026 (mptt) REVERT: B 297 PHE cc_start: 0.8481 (t80) cc_final: 0.8235 (t80) REVERT: B 370 MET cc_start: 0.7608 (pmm) cc_final: 0.7222 (pmm) REVERT: B 441 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8880 (mp) REVERT: B 478 GLN cc_start: 0.8366 (tt0) cc_final: 0.7928 (tt0) outliers start: 48 outliers final: 34 residues processed: 321 average time/residue: 0.1919 time to fit residues: 88.9991 Evaluate side-chains 306 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 93 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 182 ASN A 344 HIS A 610 GLN B 195 HIS B 229 HIS B 244 ASN B 467 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.148406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124577 restraints weight = 16768.506| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.77 r_work: 0.3583 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10016 Z= 0.125 Angle : 0.654 11.825 13650 Z= 0.308 Chirality : 0.044 0.237 1613 Planarity : 0.004 0.049 1680 Dihedral : 6.693 56.166 1706 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.24), residues: 1179 helix: 0.31 (0.25), residues: 444 sheet: -1.45 (0.49), residues: 116 loop : -1.48 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 476 HIS 0.012 0.001 HIS B 229 PHE 0.036 0.001 PHE B 347 TYR 0.019 0.001 TYR B 158 ARG 0.006 0.001 ARG A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 14) link_NAG-ASN : angle 1.18057 ( 42) link_BETA1-4 : bond 0.00491 ( 6) link_BETA1-4 : angle 1.68843 ( 18) hydrogen bonds : bond 0.04150 ( 348) hydrogen bonds : angle 4.42030 ( 1032) SS BOND : bond 0.00649 ( 5) SS BOND : angle 1.91781 ( 10) covalent geometry : bond 0.00283 ( 9991) covalent geometry : angle 0.64773 (13580) *********************** 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 329 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8084 (t0) cc_final: 0.7734 (t0) REVERT: A 103 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7710 (mmtt) REVERT: A 132 MET cc_start: 0.7353 (tmm) cc_final: 0.7097 (tmm) REVERT: A 183 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8146 (mtmm) REVERT: A 493 LEU cc_start: 0.9183 (tp) cc_final: 0.8859 (tp) REVERT: A 494 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8059 (mmmt) REVERT: A 545 ARG cc_start: 0.8461 (tpm170) cc_final: 0.8125 (tpm170) REVERT: A 644 ARG cc_start: 0.8738 (ptt90) cc_final: 0.8169 (ptt-90) REVERT: B 186 MET cc_start: 0.8778 (tpp) cc_final: 0.8150 (ttp) REVERT: B 189 LYS cc_start: 0.8447 (ttmm) cc_final: 0.7948 (mptt) REVERT: B 244 ASN cc_start: 0.8821 (m110) cc_final: 0.8536 (m110) REVERT: B 297 PHE cc_start: 0.8516 (t80) cc_final: 0.8268 (t80) REVERT: B 370 MET cc_start: 0.7466 (pmm) cc_final: 0.7082 (pmm) REVERT: B 441 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8843 (mp) REVERT: B 478 GLN cc_start: 0.8278 (tt0) cc_final: 0.7871 (tt0) outliers start: 36 outliers final: 22 residues processed: 312 average time/residue: 0.2112 time to fit residues: 96.1116 Evaluate side-chains 303 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 301 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 650 CYS 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 113 MET Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 267 ILE 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 95 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.147367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123673 restraints weight = 16751.881| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.78 r_work: 0.3567 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10016 Z= 0.122 Angle : 0.641 11.324 13650 Z= 0.300 Chirality : 0.044 0.242 1613 Planarity : 0.004 0.050 1680 Dihedral : 5.734 56.975 1703 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 4.90 % Allowed : 23.92 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1179 helix: 0.61 (0.25), residues: 442 sheet: -1.44 (0.50), residues: 116 loop : -1.34 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 476 HIS 0.004 0.001 HIS B 475 PHE 0.035 0.001 PHE B 347 TYR 0.019 0.001 TYR B 158 ARG 0.004 0.000 ARG A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 14) link_NAG-ASN : angle 1.19906 ( 42) link_BETA1-4 : bond 0.00397 ( 6) link_BETA1-4 : angle 1.69529 ( 18) hydrogen bonds : bond 0.03913 ( 348) hydrogen bonds : angle 4.30281 ( 1032) SS BOND : bond 0.00370 ( 5) SS BOND : angle 1.61775 ( 10) covalent geometry : bond 0.00279 ( 9991) covalent geometry : angle 0.63434 (13580) *********************** 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 339 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 287 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7997 (t0) cc_final: 0.7680 (t0) REVERT: A 183 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8161 (mtmm) REVERT: A 464 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 493 LEU cc_start: 0.9110 (tp) cc_final: 0.8863 (tp) REVERT: A 494 LYS cc_start: 0.8634 (mmmm) cc_final: 0.7961 (mmmt) REVERT: A 519 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8150 (pt) REVERT: A 545 ARG cc_start: 0.8525 (tpm170) cc_final: 0.8166 (tpm170) REVERT: A 627 GLU cc_start: 0.8119 (mp0) cc_final: 0.7858 (mp0) REVERT: A 644 ARG cc_start: 0.8736 (ptt90) cc_final: 0.8255 (ptt-90) REVERT: B 186 MET cc_start: 0.8633 (tpp) cc_final: 0.8053 (ttp) REVERT: B 189 LYS cc_start: 0.8552 (ttmm) cc_final: 0.7962 (mptt) REVERT: B 297 PHE cc_start: 0.8457 (t80) cc_final: 0.8204 (t80) REVERT: B 370 MET cc_start: 0.7491 (pmm) cc_final: 0.7059 (pmm) REVERT: B 441 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8898 (mp) REVERT: B 465 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: B 478 GLN cc_start: 0.8237 (tt0) cc_final: 0.7769 (tt0) outliers start: 52 outliers final: 31 residues processed: 316 average time/residue: 0.2450 time to fit residues: 114.2174 Evaluate side-chains 311 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP 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 464 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 575 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 ILE 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 441 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS A 517 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 284 ASN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.144305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119703 restraints weight = 16890.244| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.85 r_work: 0.3497 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10016 Z= 0.169 Angle : 0.669 10.609 13650 Z= 0.318 Chirality : 0.045 0.240 1613 Planarity : 0.004 0.049 1680 Dihedral : 5.728 58.159 1703 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 6.03 % Allowed : 24.48 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1179 helix: 0.64 (0.25), residues: 443 sheet: -1.54 (0.50), residues: 118 loop : -1.27 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 476 HIS 0.006 0.001 HIS B 229 PHE 0.035 0.002 PHE B 347 TYR 0.020 0.002 TYR B 158 ARG 0.006 0.000 ARG A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 14) link_NAG-ASN : angle 1.26326 ( 42) link_BETA1-4 : bond 0.00309 ( 6) link_BETA1-4 : angle 1.61739 ( 18) hydrogen bonds : bond 0.04237 ( 348) hydrogen bonds : angle 4.41813 ( 1032) SS BOND : bond 0.00437 ( 5) SS BOND : angle 2.40398 ( 10) covalent geometry : bond 0.00400 ( 9991) covalent geometry : angle 0.66095 (13580) *********************** 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 343 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8122 (t0) cc_final: 0.7797 (t0) REVERT: A 132 MET cc_start: 0.7411 (tmm) cc_final: 0.7084 (tmm) REVERT: A 173 ASN cc_start: 0.8776 (m-40) cc_final: 0.8475 (m110) REVERT: A 183 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8387 (mmmm) REVERT: A 266 GLU cc_start: 0.8459 (tt0) cc_final: 0.8079 (tt0) REVERT: A 388 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8313 (p) REVERT: A 471 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8064 (mm110) REVERT: A 493 LEU cc_start: 0.9120 (tp) cc_final: 0.8886 (tp) REVERT: A 494 LYS cc_start: 0.8710 (mmmm) cc_final: 0.7998 (mmmt) REVERT: A 514 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8433 (pt) REVERT: A 519 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8140 (pt) REVERT: A 644 ARG cc_start: 0.8793 (ptt90) cc_final: 0.7860 (ptt-90) REVERT: A 645 PHE cc_start: 0.8651 (m-80) cc_final: 0.7849 (m-80) REVERT: B 75 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8127 (t80) REVERT: B 113 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7273 (ptt) REVERT: B 139 MET cc_start: 0.8983 (mmm) cc_final: 0.8458 (mmm) REVERT: B 179 MET cc_start: 0.9106 (tpp) cc_final: 0.8657 (tpp) REVERT: B 186 MET cc_start: 0.8724 (tpp) cc_final: 0.8040 (ttp) REVERT: B 189 LYS cc_start: 0.8449 (ttmm) cc_final: 0.7948 (mptt) REVERT: B 441 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8896 (mp) outliers start: 64 outliers final: 41 residues processed: 314 average time/residue: 0.2159 time to fit residues: 99.3673 Evaluate side-chains 320 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE 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 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 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 543 LEU Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 113 MET 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 354 VAL 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 464 LYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 505 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.118937 restraints weight = 16858.994| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.65 r_work: 0.3496 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10016 Z= 0.163 Angle : 0.681 9.803 13650 Z= 0.321 Chirality : 0.045 0.239 1613 Planarity : 0.004 0.050 1680 Dihedral : 5.590 59.683 1699 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 6.59 % Allowed : 24.76 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1179 helix: 0.80 (0.25), residues: 437 sheet: -1.66 (0.50), residues: 118 loop : -1.20 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 476 HIS 0.006 0.001 HIS B 229 PHE 0.036 0.001 PHE B 347 TYR 0.021 0.002 TYR B 158 ARG 0.005 0.000 ARG A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 14) link_NAG-ASN : angle 1.26966 ( 42) link_BETA1-4 : bond 0.00348 ( 6) link_BETA1-4 : angle 1.55919 ( 18) hydrogen bonds : bond 0.04275 ( 348) hydrogen bonds : angle 4.41836 ( 1032) SS BOND : bond 0.00396 ( 5) SS BOND : angle 1.68068 ( 10) covalent geometry : bond 0.00385 ( 9991) covalent geometry : angle 0.67564 (13580) *********************** 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 357 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 287 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8094 (p0) cc_final: 0.7843 (p0) REVERT: A 82 ASP cc_start: 0.8157 (t0) cc_final: 0.7828 (t0) REVERT: A 132 MET cc_start: 0.7401 (tmm) cc_final: 0.7198 (tmm) REVERT: A 173 ASN cc_start: 0.8816 (m-40) cc_final: 0.8533 (m110) REVERT: A 183 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8356 (mmmm) REVERT: A 266 GLU cc_start: 0.8458 (tt0) cc_final: 0.8032 (tt0) REVERT: A 388 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 471 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8063 (mm110) REVERT: A 514 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8577 (pt) REVERT: A 519 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8297 (pt) REVERT: A 531 GLU cc_start: 0.8772 (mp0) cc_final: 0.8557 (mp0) REVERT: A 545 ARG cc_start: 0.8227 (tpt90) cc_final: 0.7959 (tpt90) REVERT: A 627 GLU cc_start: 0.8093 (mp0) cc_final: 0.7879 (mp0) REVERT: A 644 ARG cc_start: 0.8792 (ptt90) cc_final: 0.8246 (ptt-90) REVERT: B 75 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8109 (t80) REVERT: B 113 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7358 (ptt) REVERT: B 139 MET cc_start: 0.8992 (mmm) cc_final: 0.8054 (mmm) REVERT: B 179 MET cc_start: 0.9106 (tpp) cc_final: 0.8374 (tpp) REVERT: B 186 MET cc_start: 0.8753 (tpp) cc_final: 0.8050 (ttp) REVERT: B 189 LYS cc_start: 0.8506 (ttmm) cc_final: 0.7960 (mptt) REVERT: B 243 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8914 (tt) REVERT: B 316 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: B 441 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8918 (mp) outliers start: 70 outliers final: 44 residues processed: 325 average time/residue: 0.1952 time to fit residues: 92.0113 Evaluate side-chains 325 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 193 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 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 472 LEU 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 565 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 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 359 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 389 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116184 restraints weight = 16856.688| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.62 r_work: 0.3457 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3472 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= 0.193 Angle : 0.711 10.340 13650 Z= 0.338 Chirality : 0.046 0.234 1613 Planarity : 0.004 0.051 1680 Dihedral : 5.749 57.663 1699 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 6.78 % Allowed : 25.14 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1179 helix: 0.89 (0.25), residues: 431 sheet: -1.78 (0.49), residues: 118 loop : -1.07 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 476 HIS 0.011 0.001 HIS A 725 PHE 0.035 0.002 PHE B 347 TYR 0.022 0.002 TYR B 158 ARG 0.006 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 14) link_NAG-ASN : angle 1.38400 ( 42) link_BETA1-4 : bond 0.00393 ( 6) link_BETA1-4 : angle 1.65861 ( 18) hydrogen bonds : bond 0.04546 ( 348) hydrogen bonds : angle 4.56200 ( 1032) SS BOND : bond 0.00420 ( 5) SS BOND : angle 1.55870 ( 10) covalent geometry : bond 0.00454 ( 9991) covalent geometry : angle 0.70511 (13580) *********************** 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 345 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8232 (t0) cc_final: 0.7894 (t0) REVERT: A 132 MET cc_start: 0.7520 (tmm) cc_final: 0.7299 (tmm) REVERT: A 173 ASN cc_start: 0.8838 (m-40) cc_final: 0.8598 (m110) REVERT: A 183 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8357 (mmmm) REVERT: A 195 LEU cc_start: 0.8930 (mt) cc_final: 0.8683 (mp) REVERT: A 266 GLU cc_start: 0.8472 (tt0) cc_final: 0.8029 (tt0) REVERT: A 388 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8450 (p) REVERT: A 471 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8024 (mm110) REVERT: A 514 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8503 (pt) REVERT: A 531 GLU cc_start: 0.8835 (mp0) cc_final: 0.8617 (mp0) REVERT: A 627 GLU cc_start: 0.8028 (mp0) cc_final: 0.7663 (mp0) REVERT: B 75 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.7912 (t80) REVERT: B 157 ARG cc_start: 0.7514 (tpt-90) cc_final: 0.7135 (tpt-90) REVERT: B 186 MET cc_start: 0.8711 (tpp) cc_final: 0.8044 (ttp) REVERT: B 189 LYS cc_start: 0.8486 (ttmm) cc_final: 0.7949 (mptt) REVERT: B 243 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8870 (tt) REVERT: B 316 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: B 441 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8905 (mp) outliers start: 72 outliers final: 47 residues processed: 314 average time/residue: 0.2086 time to fit residues: 97.5842 Evaluate side-chains 316 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 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 710 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 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 359 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 389 SER 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 513 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 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 = 0.3918 r_free = 0.3918 target = 0.143358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119453 restraints weight = 16809.920| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.71 r_work: 0.3496 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10016 Z= 0.128 Angle : 0.690 10.465 13650 Z= 0.321 Chirality : 0.044 0.235 1613 Planarity : 0.004 0.051 1680 Dihedral : 5.489 57.599 1699 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 5.08 % Allowed : 27.59 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1179 helix: 0.86 (0.25), residues: 437 sheet: -1.76 (0.50), residues: 118 loop : -1.08 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 137 HIS 0.010 0.001 HIS A 725 PHE 0.036 0.001 PHE B 347 TYR 0.020 0.001 TYR B 158 ARG 0.006 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 14) link_NAG-ASN : angle 1.24510 ( 42) link_BETA1-4 : bond 0.00398 ( 6) link_BETA1-4 : angle 1.49129 ( 18) hydrogen bonds : bond 0.04148 ( 348) hydrogen bonds : angle 4.44729 ( 1032) SS BOND : bond 0.00316 ( 5) SS BOND : angle 1.29980 ( 10) covalent geometry : bond 0.00297 ( 9991) covalent geometry : angle 0.68490 (13580) *********************** 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 335 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8251 (t0) cc_final: 0.7898 (t0) REVERT: A 132 MET cc_start: 0.7368 (tmm) cc_final: 0.7122 (tmm) REVERT: A 173 ASN cc_start: 0.8818 (m-40) cc_final: 0.8578 (m110) REVERT: A 183 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8344 (mmmm) REVERT: A 266 GLU cc_start: 0.8490 (tt0) cc_final: 0.8056 (tt0) REVERT: A 388 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8439 (p) REVERT: A 433 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8318 (tp40) REVERT: A 439 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8720 (mt) REVERT: A 471 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7946 (mm110) REVERT: A 531 GLU cc_start: 0.8785 (mp0) cc_final: 0.8564 (mp0) REVERT: A 627 GLU cc_start: 0.7990 (mp0) cc_final: 0.7622 (mp0) REVERT: A 661 TRP cc_start: 0.8638 (t60) cc_final: 0.8176 (t60) REVERT: B 75 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7703 (t80) REVERT: B 124 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6318 (tt) REVERT: B 139 MET cc_start: 0.9162 (tpp) cc_final: 0.8266 (mmm) REVERT: B 179 MET cc_start: 0.9057 (tpp) cc_final: 0.8603 (tpp) REVERT: B 186 MET cc_start: 0.8737 (tpp) cc_final: 0.8009 (ttp) REVERT: B 189 LYS cc_start: 0.8509 (ttmm) cc_final: 0.7984 (mptt) REVERT: B 243 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8884 (tt) REVERT: B 316 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: B 399 LEU cc_start: 0.7686 (tp) cc_final: 0.7432 (tp) REVERT: B 441 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8921 (mp) outliers start: 54 outliers final: 37 residues processed: 313 average time/residue: 0.1799 time to fit residues: 82.8206 Evaluate side-chains 316 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 193 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 347 ILE 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 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 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 124 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.138568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114241 restraints weight = 16845.386| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.62 r_work: 0.3432 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10016 Z= 0.230 Angle : 0.769 11.813 13650 Z= 0.363 Chirality : 0.049 0.232 1613 Planarity : 0.005 0.051 1680 Dihedral : 5.884 58.351 1699 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 5.08 % Allowed : 27.78 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1179 helix: 0.85 (0.25), residues: 431 sheet: -1.89 (0.49), residues: 118 loop : -1.09 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 476 HIS 0.012 0.001 HIS A 725 PHE 0.037 0.002 PHE B 347 TYR 0.020 0.002 TYR B 158 ARG 0.006 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 14) link_NAG-ASN : angle 1.47425 ( 42) link_BETA1-4 : bond 0.00355 ( 6) link_BETA1-4 : angle 1.74415 ( 18) hydrogen bonds : bond 0.04780 ( 348) hydrogen bonds : angle 4.66718 ( 1032) SS BOND : bond 0.00422 ( 5) SS BOND : angle 1.50661 ( 10) covalent geometry : bond 0.00541 ( 9991) covalent geometry : angle 0.76336 (13580) *********************** 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 323 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8197 (t0) cc_final: 0.7885 (t0) REVERT: A 95 LEU cc_start: 0.9249 (tp) cc_final: 0.9000 (mm) REVERT: A 132 MET cc_start: 0.7555 (tmm) cc_final: 0.7217 (tmm) REVERT: A 183 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8373 (mmmm) REVERT: A 266 GLU cc_start: 0.8525 (tt0) cc_final: 0.8024 (tt0) REVERT: A 388 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 433 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8367 (tp40) REVERT: A 471 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7998 (mm110) REVERT: A 514 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8490 (pt) REVERT: A 531 GLU cc_start: 0.8846 (mp0) cc_final: 0.8607 (mp0) REVERT: A 627 GLU cc_start: 0.8006 (mp0) cc_final: 0.7646 (mp0) REVERT: A 725 HIS cc_start: 0.7982 (t-90) cc_final: 0.7721 (t-90) REVERT: B 189 LYS cc_start: 0.8469 (ttmm) cc_final: 0.7944 (mptt) REVERT: B 243 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8828 (tt) REVERT: B 316 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: B 337 ASP cc_start: 0.8769 (t0) cc_final: 0.8536 (t0) REVERT: B 441 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8883 (mp) outliers start: 54 outliers final: 38 residues processed: 305 average time/residue: 0.2187 time to fit residues: 98.1951 Evaluate side-chains 309 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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 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 660 ASN Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** 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 = 0.3892 r_free = 0.3892 target = 0.140177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115772 restraints weight = 16821.035| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.67 r_work: 0.3456 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3793 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= 0.168 Angle : 0.743 11.586 13650 Z= 0.347 Chirality : 0.047 0.231 1613 Planarity : 0.004 0.056 1680 Dihedral : 5.744 56.443 1699 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 4.52 % Allowed : 28.81 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1179 helix: 0.81 (0.25), residues: 429 sheet: -1.88 (0.49), residues: 118 loop : -1.07 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 476 HIS 0.013 0.001 HIS A 725 PHE 0.035 0.002 PHE B 347 TYR 0.021 0.002 TYR B 158 ARG 0.005 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 14) link_NAG-ASN : angle 1.35893 ( 42) link_BETA1-4 : bond 0.00380 ( 6) link_BETA1-4 : angle 1.61515 ( 18) hydrogen bonds : bond 0.04493 ( 348) hydrogen bonds : angle 4.58297 ( 1032) SS BOND : bond 0.00342 ( 5) SS BOND : angle 1.34580 ( 10) covalent geometry : bond 0.00400 ( 9991) covalent geometry : angle 0.73782 (13580) ********************** 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 330 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.8194 (t0) cc_final: 0.7924 (t0) REVERT: A 95 LEU cc_start: 0.9261 (tp) cc_final: 0.9014 (mm) REVERT: A 132 MET cc_start: 0.7427 (tmm) cc_final: 0.7095 (tmm) REVERT: A 183 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8386 (mmmm) REVERT: A 266 GLU cc_start: 0.8480 (tt0) cc_final: 0.8007 (tt0) REVERT: A 388 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 433 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8325 (tp40) REVERT: A 471 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7882 (mm110) REVERT: A 531 GLU cc_start: 0.8825 (mp0) cc_final: 0.8594 (mp0) REVERT: A 627 GLU cc_start: 0.8043 (mp0) cc_final: 0.7690 (mp0) REVERT: A 661 TRP cc_start: 0.8623 (t60) cc_final: 0.8275 (t60) REVERT: A 725 HIS cc_start: 0.7949 (t-90) cc_final: 0.7711 (t-90) REVERT: B 75 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 186 MET cc_start: 0.8673 (tpp) cc_final: 0.8003 (ttp) REVERT: B 189 LYS cc_start: 0.8531 (ttmm) cc_final: 0.7998 (mptt) REVERT: B 243 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 337 ASP cc_start: 0.8734 (t0) cc_final: 0.8507 (t0) outliers start: 48 outliers final: 37 residues processed: 313 average time/residue: 0.1864 time to fit residues: 85.6794 Evaluate side-chains 319 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain A residue 347 ILE 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 446 GLN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 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 708 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.143421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119584 restraints weight = 16924.803| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.71 r_work: 0.3503 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10016 Z= 0.129 Angle : 0.737 10.765 13650 Z= 0.342 Chirality : 0.046 0.233 1613 Planarity : 0.005 0.064 1680 Dihedral : 5.434 56.120 1699 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 3.86 % Allowed : 29.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1179 helix: 0.92 (0.26), residues: 424 sheet: -1.84 (0.49), residues: 118 loop : -1.03 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 477 HIS 0.012 0.001 HIS A 725 PHE 0.036 0.001 PHE B 347 TYR 0.025 0.001 TYR B 158 ARG 0.006 0.000 ARG A 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 14) link_NAG-ASN : angle 1.25780 ( 42) link_BETA1-4 : bond 0.00407 ( 6) link_BETA1-4 : angle 1.50477 ( 18) hydrogen bonds : bond 0.04095 ( 348) hydrogen bonds : angle 4.46640 ( 1032) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.99355 ( 10) covalent geometry : bond 0.00298 ( 9991) covalent geometry : angle 0.73266 (13580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6633.97 seconds wall clock time: 118 minutes 57.27 seconds (7137.27 seconds total)