Starting phenix.real_space_refine on Wed Mar 4 01:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c76_30293/03_2026/7c76_30293.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c76_30293/03_2026/7c76_30293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c76_30293/03_2026/7c76_30293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c76_30293/03_2026/7c76_30293.map" model { file = "/net/cci-nas-00/data/ceres_data/7c76_30293/03_2026/7c76_30293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c76_30293/03_2026/7c76_30293.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6318 2.51 5 N 1600 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5563 Classifications: {'peptide': 691} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3855 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "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: 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.29, per 1000 atoms: 0.23 Number of scatterers: 9762 At special positions: 0 Unit cell: (135.705, 176.79, 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 40 16.00 O 1804 8.00 N 1600 7.00 C 6318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.04 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 651 " - pdb=" SG CYS A 696 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1001 " - " ASN A 52 " " NAG A1002 " - " ASN A 57 " " NAG A1003 " - " ASN A 70 " " NAG A1004 " - " ASN A 124 " " NAG A1005 " - " ASN A 196 " " NAG A1013 " - " ASN A 265 " " NAG A1014 " - " ASN A 291 " " NAG A1022 " - " ASN A 662 " " NAG B 601 " - " ASN B 251 " " NAG C 1 " - " ASN A 247 " " NAG D 1 " - " ASN A 252 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 413 " " NAG G 1 " - " ASN A 398 " " NAG H 1 " - " ASN A 507 " " NAG I 1 " - " ASN B 272 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 391.2 milliseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 42.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.592A pdb=" N THR A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.298A pdb=" N CYS A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.615A pdb=" N THR A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 120 " --> pdb=" O LYS A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 120' Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.568A pdb=" N LEU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.641A pdb=" N ILE A 220 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.681A pdb=" N LYS A 272 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 632 through 635 removed outlier: 3.685A pdb=" N ARG A 635 " --> pdb=" O PRO A 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 635' Processing helix chain 'A' and resid 650 through 663 removed outlier: 6.301A pdb=" N TRP A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 701 through 726 Processing helix chain 'B' and resid 46 through 89 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 117 through 123 removed outlier: 4.350A pdb=" N ALA B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 157 through 199 Proline residue: B 163 - end of helix removed outlier: 4.582A 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: 3.935A pdb=" N VAL B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.992A pdb=" N THR B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.554A pdb=" N SER B 264 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 306 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.546A pdb=" N GLU B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.903A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE B 328 " --> pdb=" O TRP B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 328' 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 365 through 370 removed outlier: 4.429A pdb=" N SER B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 374 through 396 removed outlier: 3.633A pdb=" N LEU B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 422 removed outlier: 4.297A pdb=" N LEU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 461 removed outlier: 3.881A pdb=" N TYR B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.772A 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 518 removed outlier: 3.766A pdb=" N LEU B 518 " --> pdb=" O MET B 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.243A pdb=" N ALA A 35 " --> pdb=" O ASN A 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.869A pdb=" N LEU A 128 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA6, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.914A pdb=" N LEU A 226 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 253 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 279 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 327 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE A 461 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA9, first strand: chain 'A' and resid 395 through 396 Processing sheet with id=AB1, first strand: chain 'A' and resid 444 through 446 Processing sheet with id=AB2, first strand: chain 'A' and resid 614 through 616 349 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3031 1.35 - 1.46: 2472 1.46 - 1.58: 4424 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 9992 Sorted by residual: bond pdb=" C PRO B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 4.14e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 9987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 13136 1.58 - 3.15: 359 3.15 - 4.73: 53 4.73 - 6.30: 21 6.30 - 7.88: 4 Bond angle restraints: 13573 Sorted by residual: angle pdb=" C ASN A 140 " pdb=" N ASN A 141 " pdb=" CA ASN A 141 " ideal model delta sigma weight residual 121.80 129.06 -7.26 2.44e+00 1.68e-01 8.86e+00 angle pdb=" N ASN A 141 " pdb=" CA ASN A 141 " pdb=" C ASN A 141 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.03e+00 angle pdb=" CA LEU B 500 " pdb=" CB LEU B 500 " pdb=" CG LEU B 500 " ideal model delta sigma weight residual 116.30 124.18 -7.88 3.50e+00 8.16e-02 5.07e+00 angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" C PRO B 208 " ideal model delta sigma weight residual 110.70 113.31 -2.61 1.22e+00 6.72e-01 4.59e+00 angle pdb=" N THR B 126 " pdb=" CA THR B 126 " pdb=" C THR B 126 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.50e+00 ... (remaining 13568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 5628 21.75 - 43.51: 516 43.51 - 65.26: 61 65.26 - 87.01: 27 87.01 - 108.77: 11 Dihedral angle restraints: 6243 sinusoidal: 2807 harmonic: 3436 Sorted by residual: dihedral pdb=" CA PRO B 208 " pdb=" C PRO B 208 " pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 95 " pdb=" SG CYS A 95 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -48.50 -37.50 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.94 108.77 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 6240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1395 0.058 - 0.116: 212 0.116 - 0.174: 12 0.174 - 0.232: 1 0.232 - 0.290: 3 Chirality restraints: 1623 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 247 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1620 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 312 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 313 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 207 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 208 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 208 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 209 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " 0.024 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1208 2.76 - 3.29: 9743 3.29 - 3.83: 16679 3.83 - 4.36: 18951 4.36 - 4.90: 32613 Nonbonded interactions: 79194 Sorted by model distance: nonbonded pdb=" O HIS B 229 " pdb=" OG SER B 383 " model vdw 2.219 3.040 nonbonded pdb=" O ASP A 347 " pdb=" OG SER A 350 " model vdw 2.267 3.040 nonbonded pdb=" O LEU A 637 " pdb=" OG1 THR A 666 " model vdw 2.272 3.040 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 178 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU B 353 " pdb=" OG SER B 446 " model vdw 2.278 3.040 ... (remaining 79189 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 'C' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' 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: 0.640 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 0.034 10021 Z= 0.165 Angle : 0.632 7.878 13656 Z= 0.305 Chirality : 0.043 0.290 1623 Planarity : 0.003 0.048 1672 Dihedral : 16.860 108.767 4011 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 1.91 % Allowed : 10.22 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.23), residues: 1168 helix: -0.53 (0.24), residues: 418 sheet: -3.24 (0.43), residues: 120 loop : -2.51 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 51 TYR 0.011 0.001 TYR B 248 PHE 0.013 0.001 PHE A 647 TRP 0.006 0.001 TRP B 476 HIS 0.009 0.000 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9992) covalent geometry : angle 0.62861 (13573) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.31183 ( 8) hydrogen bonds : bond 0.15708 ( 349) hydrogen bonds : angle 5.94682 ( 1005) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 1.15771 ( 27) link_NAG-ASN : bond 0.00274 ( 16) link_NAG-ASN : angle 0.97459 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7441 (mpp) cc_final: 0.7150 (mpp) REVERT: B 55 ARG cc_start: 0.7440 (mtt-85) cc_final: 0.7200 (ptp-110) REVERT: B 123 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6549 (tt) REVERT: B 189 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8014 (mmtm) REVERT: B 268 LEU cc_start: 0.7170 (mt) cc_final: 0.6813 (pp) REVERT: B 332 PHE cc_start: 0.8100 (m-80) cc_final: 0.7054 (m-80) REVERT: B 476 TRP cc_start: 0.9017 (t60) cc_final: 0.8726 (t60) REVERT: B 513 ARG cc_start: 0.7599 (tmt170) cc_final: 0.6853 (tmt170) REVERT: B 514 MET cc_start: 0.6661 (mtm) cc_final: 0.5459 (mtt) outliers start: 20 outliers final: 7 residues processed: 332 average time/residue: 0.0788 time to fit residues: 38.6470 Evaluate side-chains 282 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 274 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 702 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 169 GLN A 299 GLN A 410 HIS ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 213 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.153774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127306 restraints weight = 15794.932| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.51 r_work: 0.3525 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10021 Z= 0.159 Angle : 0.671 10.103 13656 Z= 0.315 Chirality : 0.046 0.278 1623 Planarity : 0.004 0.044 1672 Dihedral : 7.911 63.782 1793 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 2.67 % Allowed : 17.29 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.25), residues: 1168 helix: 0.49 (0.26), residues: 432 sheet: -3.01 (0.47), residues: 110 loop : -1.94 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 374 TYR 0.018 0.002 TYR B 349 PHE 0.021 0.001 PHE B 483 TRP 0.016 0.001 TRP A 656 HIS 0.010 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9992) covalent geometry : angle 0.66359 (13573) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.97102 ( 8) hydrogen bonds : bond 0.04092 ( 349) hydrogen bonds : angle 4.35523 ( 1005) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.72962 ( 27) link_NAG-ASN : bond 0.00268 ( 16) link_NAG-ASN : angle 1.33669 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 293 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 193 ILE cc_start: 0.8965 (pt) cc_final: 0.8746 (mp) REVERT: A 364 ASP cc_start: 0.8306 (t0) cc_final: 0.7923 (t0) REVERT: A 416 LYS cc_start: 0.8804 (mttt) cc_final: 0.8397 (mttp) REVERT: A 626 GLU cc_start: 0.8329 (pt0) cc_final: 0.7810 (pp20) REVERT: B 132 PHE cc_start: 0.8599 (t80) cc_final: 0.8327 (t80) REVERT: B 189 LYS cc_start: 0.8418 (mtpt) cc_final: 0.7698 (mmtm) REVERT: B 268 LEU cc_start: 0.6929 (mt) cc_final: 0.6623 (pp) REVERT: B 462 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7537 (mp0) REVERT: B 473 ILE cc_start: 0.9141 (mt) cc_final: 0.8929 (mp) REVERT: B 476 TRP cc_start: 0.9167 (t60) cc_final: 0.8611 (t60) REVERT: B 513 ARG cc_start: 0.7788 (tmt170) cc_final: 0.7489 (tmt170) REVERT: B 514 MET cc_start: 0.6211 (mtm) cc_final: 0.5160 (mtt) outliers start: 28 outliers final: 20 residues processed: 308 average time/residue: 0.0780 time to fit residues: 35.5929 Evaluate side-chains 282 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 97 optimal weight: 0.0980 chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 475 HIS ** 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 = 0.3972 r_free = 0.3972 target = 0.151768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124730 restraints weight = 15807.409| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.54 r_work: 0.3494 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10021 Z= 0.142 Angle : 0.644 9.429 13656 Z= 0.300 Chirality : 0.044 0.262 1623 Planarity : 0.004 0.045 1672 Dihedral : 6.337 52.482 1787 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 3.34 % Allowed : 20.25 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.25), residues: 1168 helix: 0.88 (0.26), residues: 428 sheet: -3.01 (0.47), residues: 110 loop : -1.73 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 513 TYR 0.017 0.001 TYR B 349 PHE 0.015 0.001 PHE A 706 TRP 0.012 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9992) covalent geometry : angle 0.63579 (13573) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.72758 ( 8) hydrogen bonds : bond 0.03856 ( 349) hydrogen bonds : angle 4.16926 ( 1005) link_BETA1-4 : bond 0.00308 ( 9) link_BETA1-4 : angle 1.63950 ( 27) link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 1.48425 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8473 (t0) cc_final: 0.8016 (t0) REVERT: A 471 LEU cc_start: 0.9160 (mm) cc_final: 0.8956 (mt) REVERT: A 626 GLU cc_start: 0.8334 (pt0) cc_final: 0.8027 (mt-10) REVERT: B 132 PHE cc_start: 0.8734 (t80) cc_final: 0.8498 (t80) REVERT: B 189 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7801 (mmtm) REVERT: B 268 LEU cc_start: 0.6928 (mt) cc_final: 0.6680 (pp) REVERT: B 320 ARG cc_start: 0.7605 (mmp80) cc_final: 0.7254 (mmp80) REVERT: B 334 HIS cc_start: 0.9278 (m170) cc_final: 0.8737 (m-70) REVERT: B 365 TYR cc_start: 0.8713 (m-80) cc_final: 0.8388 (m-80) REVERT: B 462 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7678 (mp0) REVERT: B 473 ILE cc_start: 0.9099 (mt) cc_final: 0.8854 (mp) REVERT: B 476 TRP cc_start: 0.9205 (t60) cc_final: 0.8653 (t60) REVERT: B 513 ARG cc_start: 0.8045 (tmt170) cc_final: 0.7670 (tmt170) REVERT: B 514 MET cc_start: 0.6254 (mtm) cc_final: 0.5449 (mtm) REVERT: B 517 LYS cc_start: 0.7416 (ptpt) cc_final: 0.7118 (ptpt) REVERT: B 519 ARG cc_start: 0.8162 (mmp80) cc_final: 0.7763 (tpp-160) outliers start: 35 outliers final: 24 residues processed: 289 average time/residue: 0.0771 time to fit residues: 33.5984 Evaluate side-chains 281 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 92 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.152812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126186 restraints weight = 15729.396| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.47 r_work: 0.3512 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10021 Z= 0.109 Angle : 0.610 8.559 13656 Z= 0.285 Chirality : 0.043 0.247 1623 Planarity : 0.004 0.050 1672 Dihedral : 5.202 52.097 1786 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 3.92 % Allowed : 20.44 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.25), residues: 1168 helix: 1.09 (0.26), residues: 429 sheet: -2.93 (0.47), residues: 110 loop : -1.57 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 222 TYR 0.017 0.001 TYR B 349 PHE 0.015 0.001 PHE A 294 TRP 0.010 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9992) covalent geometry : angle 0.60433 (13573) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.56157 ( 8) hydrogen bonds : bond 0.03514 ( 349) hydrogen bonds : angle 3.99680 ( 1005) link_BETA1-4 : bond 0.00365 ( 9) link_BETA1-4 : angle 1.49349 ( 27) link_NAG-ASN : bond 0.00254 ( 16) link_NAG-ASN : angle 1.13494 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8505 (t0) cc_final: 0.8268 (t0) REVERT: A 365 ASN cc_start: 0.8122 (m-40) cc_final: 0.7737 (m110) REVERT: B 132 PHE cc_start: 0.8731 (t80) cc_final: 0.8511 (t80) REVERT: B 189 LYS cc_start: 0.8574 (mtpt) cc_final: 0.7884 (mmtm) REVERT: B 268 LEU cc_start: 0.7058 (mt) cc_final: 0.6759 (pp) REVERT: B 365 TYR cc_start: 0.8740 (m-80) cc_final: 0.8412 (m-80) REVERT: B 462 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7651 (mp0) REVERT: B 473 ILE cc_start: 0.9169 (mt) cc_final: 0.8950 (mp) REVERT: B 476 TRP cc_start: 0.9177 (t60) cc_final: 0.8643 (t60) REVERT: B 513 ARG cc_start: 0.8104 (tmt170) cc_final: 0.7789 (tmt170) REVERT: B 514 MET cc_start: 0.6210 (mtm) cc_final: 0.5229 (mtm) REVERT: B 517 LYS cc_start: 0.7693 (ptpt) cc_final: 0.7493 (ptpt) outliers start: 41 outliers final: 29 residues processed: 300 average time/residue: 0.0737 time to fit residues: 33.2172 Evaluate side-chains 291 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 109 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** 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 = 0.3922 r_free = 0.3922 target = 0.147770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121046 restraints weight = 15976.956| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.49 r_work: 0.3437 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10021 Z= 0.172 Angle : 0.634 8.199 13656 Z= 0.302 Chirality : 0.044 0.286 1623 Planarity : 0.004 0.051 1672 Dihedral : 5.198 52.643 1786 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 4.20 % Allowed : 21.49 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.26), residues: 1168 helix: 1.26 (0.27), residues: 423 sheet: -2.92 (0.47), residues: 109 loop : -1.37 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.018 0.001 TYR B 349 PHE 0.016 0.001 PHE A 702 TRP 0.016 0.001 TRP B 137 HIS 0.006 0.001 HIS A 724 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9992) covalent geometry : angle 0.62687 (13573) SS BOND : bond 0.00303 ( 4) SS BOND : angle 0.76313 ( 8) hydrogen bonds : bond 0.03883 ( 349) hydrogen bonds : angle 4.03038 ( 1005) link_BETA1-4 : bond 0.00336 ( 9) link_BETA1-4 : angle 1.35079 ( 27) link_NAG-ASN : bond 0.00313 ( 16) link_NAG-ASN : angle 1.50613 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.9137 (tp) cc_final: 0.8935 (tt) REVERT: A 364 ASP cc_start: 0.8499 (t0) cc_final: 0.7983 (t0) REVERT: B 132 PHE cc_start: 0.8696 (t80) cc_final: 0.8410 (t80) REVERT: B 207 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7193 (ttp80) REVERT: B 346 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8634 (t80) REVERT: B 462 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7763 (mp0) REVERT: B 476 TRP cc_start: 0.9238 (t60) cc_final: 0.8663 (t60) REVERT: B 513 ARG cc_start: 0.8140 (tmt170) cc_final: 0.7788 (tmt170) REVERT: B 514 MET cc_start: 0.6024 (mtm) cc_final: 0.4968 (mtm) REVERT: B 517 LYS cc_start: 0.7690 (ptpt) cc_final: 0.7451 (ptpt) outliers start: 44 outliers final: 31 residues processed: 287 average time/residue: 0.0713 time to fit residues: 31.5304 Evaluate side-chains 289 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 511 TYR Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 57 optimal weight: 0.0010 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 244 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** 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 = 0.3948 r_free = 0.3948 target = 0.149713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123170 restraints weight = 15885.751| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.45 r_work: 0.3472 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10021 Z= 0.113 Angle : 0.615 9.160 13656 Z= 0.287 Chirality : 0.043 0.259 1623 Planarity : 0.004 0.053 1672 Dihedral : 5.068 52.410 1786 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 4.49 % Allowed : 22.45 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.26), residues: 1168 helix: 1.46 (0.27), residues: 412 sheet: -2.77 (0.49), residues: 109 loop : -1.30 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 489 TYR 0.020 0.001 TYR A 383 PHE 0.018 0.001 PHE B 483 TRP 0.011 0.001 TRP B 137 HIS 0.006 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9992) covalent geometry : angle 0.60895 (13573) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.62194 ( 8) hydrogen bonds : bond 0.03589 ( 349) hydrogen bonds : angle 3.95205 ( 1005) link_BETA1-4 : bond 0.00388 ( 9) link_BETA1-4 : angle 1.21992 ( 27) link_NAG-ASN : bond 0.00240 ( 16) link_NAG-ASN : angle 1.29845 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8543 (t0) cc_final: 0.8165 (t0) REVERT: A 457 ASN cc_start: 0.7996 (m-40) cc_final: 0.7392 (p0) REVERT: A 707 MET cc_start: 0.8498 (mtp) cc_final: 0.8204 (mtp) REVERT: B 123 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.7027 (tp) REVERT: B 207 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7276 (ttp80) REVERT: B 333 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8114 (mmmt) REVERT: B 346 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8532 (t80) REVERT: B 462 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7811 (mp0) REVERT: B 473 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8974 (mp) REVERT: B 476 TRP cc_start: 0.9258 (t60) cc_final: 0.8627 (t60) REVERT: B 513 ARG cc_start: 0.8100 (tmt170) cc_final: 0.7736 (tmt170) REVERT: B 514 MET cc_start: 0.6108 (mtm) cc_final: 0.5007 (mtm) REVERT: B 517 LYS cc_start: 0.7664 (ptpt) cc_final: 0.7436 (ptpt) outliers start: 47 outliers final: 37 residues processed: 298 average time/residue: 0.0732 time to fit residues: 33.2046 Evaluate side-chains 304 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** 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 = 0.3729 r_free = 0.3729 target = 0.133250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106069 restraints weight = 16375.960| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.58 r_work: 0.3218 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.065 10021 Z= 0.453 Angle : 0.947 9.503 13656 Z= 0.463 Chirality : 0.055 0.375 1623 Planarity : 0.005 0.048 1672 Dihedral : 6.562 56.477 1786 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.05 % Favored : 91.87 % Rotamer: Outliers : 5.73 % Allowed : 23.02 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.25), residues: 1168 helix: 0.98 (0.26), residues: 399 sheet: -3.12 (0.48), residues: 111 loop : -1.65 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 320 TYR 0.032 0.003 TYR B 90 PHE 0.037 0.003 PHE A 702 TRP 0.027 0.003 TRP B 137 HIS 0.012 0.002 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.01024 ( 9992) covalent geometry : angle 0.93800 (13573) SS BOND : bond 0.00745 ( 4) SS BOND : angle 1.68374 ( 8) hydrogen bonds : bond 0.05455 ( 349) hydrogen bonds : angle 4.68050 ( 1005) link_BETA1-4 : bond 0.00473 ( 9) link_BETA1-4 : angle 1.39568 ( 27) link_NAG-ASN : bond 0.00564 ( 16) link_NAG-ASN : angle 2.14398 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7884 (t0) cc_final: 0.7614 (t0) REVERT: B 106 ASP cc_start: 0.8081 (t70) cc_final: 0.7829 (t0) REVERT: B 207 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7598 (ttp80) REVERT: B 333 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8112 (mmmt) REVERT: B 346 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8786 (t80) REVERT: B 378 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8809 (tt) REVERT: B 462 GLU cc_start: 0.8614 (mt-10) cc_final: 0.7906 (mp0) REVERT: B 493 MET cc_start: 0.5085 (mmm) cc_final: 0.4864 (mmm) REVERT: B 513 ARG cc_start: 0.8174 (tmt170) cc_final: 0.7624 (tmt170) REVERT: B 517 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7423 (ptpt) outliers start: 60 outliers final: 36 residues processed: 269 average time/residue: 0.0740 time to fit residues: 30.0900 Evaluate side-chains 268 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 109 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN B 221 GLN B 244 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115982 restraints weight = 15804.790| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.48 r_work: 0.3331 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10021 Z= 0.138 Angle : 0.713 10.784 13656 Z= 0.332 Chirality : 0.047 0.274 1623 Planarity : 0.004 0.049 1672 Dihedral : 5.963 54.228 1786 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 3.34 % Allowed : 26.27 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.25), residues: 1168 helix: 1.31 (0.27), residues: 401 sheet: -2.97 (0.49), residues: 109 loop : -1.35 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 207 TYR 0.022 0.002 TYR B 349 PHE 0.018 0.002 PHE A 294 TRP 0.014 0.001 TRP A 546 HIS 0.007 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9992) covalent geometry : angle 0.70778 (13573) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.19720 ( 8) hydrogen bonds : bond 0.04241 ( 349) hydrogen bonds : angle 4.26468 ( 1005) link_BETA1-4 : bond 0.00348 ( 9) link_BETA1-4 : angle 1.14104 ( 27) link_NAG-ASN : bond 0.00243 ( 16) link_NAG-ASN : angle 1.43455 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7885 (t0) cc_final: 0.7560 (t0) REVERT: A 364 ASP cc_start: 0.8364 (t0) cc_final: 0.7814 (t0) REVERT: A 615 LEU cc_start: 0.8953 (tp) cc_final: 0.8587 (mp) REVERT: A 707 MET cc_start: 0.8520 (mtp) cc_final: 0.8252 (mtp) REVERT: B 320 ARG cc_start: 0.7856 (mmp80) cc_final: 0.5815 (ttm-80) REVERT: B 333 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8138 (mmmt) REVERT: B 346 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8621 (t80) REVERT: B 349 TYR cc_start: 0.7370 (t80) cc_final: 0.7096 (t80) REVERT: B 462 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7925 (mp0) REVERT: B 473 ILE cc_start: 0.9164 (mp) cc_final: 0.8937 (mp) REVERT: B 476 TRP cc_start: 0.9223 (t60) cc_final: 0.8671 (t60) REVERT: B 513 ARG cc_start: 0.8095 (tmt170) cc_final: 0.7675 (tmt170) REVERT: B 514 MET cc_start: 0.6102 (mtm) cc_final: 0.4949 (mtm) REVERT: B 517 LYS cc_start: 0.7618 (ptpt) cc_final: 0.7380 (ptpt) outliers start: 35 outliers final: 31 residues processed: 272 average time/residue: 0.0771 time to fit residues: 31.3281 Evaluate side-chains 274 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 110 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.142642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116037 restraints weight = 15732.879| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.49 r_work: 0.3342 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10021 Z= 0.151 Angle : 0.735 10.914 13656 Z= 0.338 Chirality : 0.046 0.272 1623 Planarity : 0.004 0.049 1672 Dihedral : 5.700 54.666 1786 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 3.72 % Allowed : 26.17 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.26), residues: 1168 helix: 1.38 (0.27), residues: 399 sheet: -2.88 (0.50), residues: 109 loop : -1.28 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 519 TYR 0.019 0.002 TYR B 349 PHE 0.017 0.001 PHE A 294 TRP 0.014 0.001 TRP B 137 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9992) covalent geometry : angle 0.72971 (13573) SS BOND : bond 0.00355 ( 4) SS BOND : angle 1.29671 ( 8) hydrogen bonds : bond 0.04027 ( 349) hydrogen bonds : angle 4.24770 ( 1005) link_BETA1-4 : bond 0.00351 ( 9) link_BETA1-4 : angle 1.19335 ( 27) link_NAG-ASN : bond 0.00214 ( 16) link_NAG-ASN : angle 1.41182 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7879 (t0) cc_final: 0.7570 (t0) REVERT: A 364 ASP cc_start: 0.8525 (t0) cc_final: 0.7990 (t0) REVERT: A 615 LEU cc_start: 0.8956 (tp) cc_final: 0.8563 (mp) REVERT: A 626 GLU cc_start: 0.8321 (pt0) cc_final: 0.7790 (pp20) REVERT: A 707 MET cc_start: 0.8541 (mtp) cc_final: 0.8252 (mtp) REVERT: B 320 ARG cc_start: 0.7967 (mmp80) cc_final: 0.5942 (ttm-80) REVERT: B 333 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8090 (mmmt) REVERT: B 346 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8617 (t80) REVERT: B 462 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7937 (mp0) REVERT: B 473 ILE cc_start: 0.9172 (mp) cc_final: 0.8944 (mp) REVERT: B 476 TRP cc_start: 0.9242 (t60) cc_final: 0.8674 (t60) REVERT: B 513 ARG cc_start: 0.8110 (tmt170) cc_final: 0.7678 (tmt170) REVERT: B 514 MET cc_start: 0.6129 (mtm) cc_final: 0.4993 (mtm) outliers start: 39 outliers final: 33 residues processed: 279 average time/residue: 0.0741 time to fit residues: 30.9742 Evaluate side-chains 281 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** 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 = 0.3822 r_free = 0.3822 target = 0.141062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114662 restraints weight = 15749.479| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.47 r_work: 0.3322 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10021 Z= 0.187 Angle : 0.755 11.035 13656 Z= 0.351 Chirality : 0.047 0.283 1623 Planarity : 0.004 0.049 1672 Dihedral : 5.733 55.290 1786 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.03 % Rotamer: Outliers : 4.01 % Allowed : 26.17 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.25), residues: 1168 helix: 1.29 (0.26), residues: 399 sheet: -2.89 (0.50), residues: 109 loop : -1.28 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 207 TYR 0.039 0.002 TYR B 349 PHE 0.017 0.002 PHE A 702 TRP 0.018 0.001 TRP B 137 HIS 0.013 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9992) covalent geometry : angle 0.74935 (13573) SS BOND : bond 0.00379 ( 4) SS BOND : angle 1.21761 ( 8) hydrogen bonds : bond 0.04276 ( 349) hydrogen bonds : angle 4.33214 ( 1005) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 1.22124 ( 27) link_NAG-ASN : bond 0.00243 ( 16) link_NAG-ASN : angle 1.50220 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7894 (t0) cc_final: 0.7573 (t0) REVERT: A 364 ASP cc_start: 0.8511 (t0) cc_final: 0.7975 (t0) REVERT: A 615 LEU cc_start: 0.8959 (tp) cc_final: 0.8579 (mp) REVERT: A 707 MET cc_start: 0.8544 (mtp) cc_final: 0.8253 (mtp) REVERT: B 333 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8094 (mmmt) REVERT: B 346 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8607 (t80) REVERT: B 462 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7933 (mp0) REVERT: B 473 ILE cc_start: 0.9120 (mp) cc_final: 0.8885 (mp) REVERT: B 476 TRP cc_start: 0.9237 (t60) cc_final: 0.8655 (t60) REVERT: B 517 LYS cc_start: 0.7461 (ptpt) cc_final: 0.7156 (ptpt) outliers start: 42 outliers final: 34 residues processed: 282 average time/residue: 0.0781 time to fit residues: 33.0197 Evaluate side-chains 287 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 102 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 73 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 11 optimal weight: 0.0770 chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** 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 = 0.3883 r_free = 0.3883 target = 0.146018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119606 restraints weight = 15667.812| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.50 r_work: 0.3391 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10021 Z= 0.125 Angle : 0.738 11.869 13656 Z= 0.337 Chirality : 0.046 0.238 1623 Planarity : 0.004 0.049 1672 Dihedral : 5.453 54.527 1786 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 2.87 % Allowed : 27.60 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.25), residues: 1168 helix: 1.30 (0.26), residues: 406 sheet: -2.82 (0.50), residues: 109 loop : -1.22 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 320 TYR 0.032 0.002 TYR B 349 PHE 0.018 0.001 PHE A 294 TRP 0.010 0.001 TRP A 546 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9992) covalent geometry : angle 0.73472 (13573) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.80339 ( 8) hydrogen bonds : bond 0.03818 ( 349) hydrogen bonds : angle 4.19889 ( 1005) link_BETA1-4 : bond 0.00375 ( 9) link_BETA1-4 : angle 1.19681 ( 27) link_NAG-ASN : bond 0.00284 ( 16) link_NAG-ASN : angle 1.23858 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.93 seconds wall clock time: 50 minutes 9.01 seconds (3009.01 seconds total)