Starting phenix.real_space_refine on Fri Sep 11 14:28:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c76_30293/09_2026/7c76_30293.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c76_30293/09_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_30293/09_2026/7c76_30293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c76_30293/09_2026/7c76_30293.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7c76_30293/09_2026/7c76_30293.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c76_30293/09_2026/7c76_30293.cif" model { file = "/net/cci-nas-00/data/ceres_data/7c76_30293/09_2026/7c76_30293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c76_30293/09_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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 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 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 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 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.68, per 1000 atoms: 0.17 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: 1.10 Conformation dependent library (CDL) restraints added in 328.5 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: 0.28 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: 1.45 Time building geometry restraints manager: 1.34 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 - 17.93: 4961 17.93 - 35.85: 601 35.85 - 53.78: 128 53.78 - 71.70: 22 71.70 - 89.63: 10 Dihedral angle restraints: 5722 sinusoidal: 2286 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=" CB CYS B 260 " pdb=" SG CYS B 260 " pdb=" SG CYS B 368 " pdb=" CB CYS B 368 " ideal model delta sinusoidal sigma weight residual 93.00 121.39 -28.39 1 1.00e+01 1.00e-02 1.15e+01 ... (remaining 5719 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 16.305 89.628 3490 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/Z covalent geometry : bond 0.00324 / 0.17 ( 9992) covalent geometry : angle 0.62861 / 0.30 (13573) SS BOND : bond 0.00293 / 0.15 ( 4) SS BOND : angle 1.31183 / 0.71 ( 8) hydrogen bonds : bond 0.15708 / 10.36 ( 349) hydrogen bonds : angle 5.94682 / 3.95 ( 1005) link_BETA1-4 : bond 0.00361 / 0.18 ( 9) link_BETA1-4 : angle 1.15771 / 0.80 ( 27) link_NAG-ASN : bond 0.00274 / 0.15 ( 16) link_NAG-ASN : angle 0.97459 / 0.60 ( 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 : 0.291 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: 0.0747 time to fit residues: 36.5482 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 : 0.330 ------------------------------------------------------------------------------- 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... 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 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 = 0.3988 r_free = 0.3988 target = 0.153503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126793 restraints weight = 15821.165| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.53 r_work: 0.3521 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10021 Z= 0.158 Angle : 0.663 10.101 13656 Z= 0.314 Chirality : 0.045 0.235 1623 Planarity : 0.004 0.043 1672 Dihedral : 4.473 50.018 1272 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 2.96 % Allowed : 16.71 % Favored : 80.32 % 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: -1.63 (0.25), residues: 1168 helix: 0.51 (0.26), residues: 432 sheet: -3.01 (0.47), residues: 110 loop : -1.93 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 374 TYR 0.017 0.002 TYR B 349 PHE 0.021 0.001 PHE B 483 TRP 0.015 0.001 TRP A 656 HIS 0.010 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9992) covalent geometry : angle 0.65692 / 0.31 (13573) SS BOND : bond 0.00293 / 0.15 ( 4) SS BOND : angle 0.96023 / 0.57 ( 8) hydrogen bonds : bond 0.03982 / 2.71 ( 349) hydrogen bonds : angle 4.33198 / 2.91 ( 1005) link_BETA1-4 : bond 0.00299 / 0.17 ( 9) link_BETA1-4 : angle 1.35223 / 1.03 ( 27) link_NAG-ASN : bond 0.00200 / 0.13 ( 16) link_NAG-ASN : angle 1.36981 / 0.82 ( 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 323 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 193 ILE cc_start: 0.8951 (pt) cc_final: 0.8733 (mp) REVERT: A 364 ASP cc_start: 0.8266 (t0) cc_final: 0.7916 (t0) REVERT: A 416 LYS cc_start: 0.8818 (mttt) cc_final: 0.8412 (mttp) REVERT: A 471 LEU cc_start: 0.9079 (mm) cc_final: 0.8856 (mt) REVERT: A 626 GLU cc_start: 0.8331 (pt0) cc_final: 0.7946 (mt-10) REVERT: B 132 PHE cc_start: 0.8612 (t80) cc_final: 0.8352 (t80) REVERT: B 189 LYS cc_start: 0.8425 (mtpt) cc_final: 0.7714 (mmtm) REVERT: B 268 LEU cc_start: 0.6934 (mt) cc_final: 0.6628 (pp) REVERT: B 462 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7549 (mp0) REVERT: B 473 ILE cc_start: 0.9152 (mt) cc_final: 0.8941 (mp) REVERT: B 476 TRP cc_start: 0.9174 (t60) cc_final: 0.8618 (t60) REVERT: B 513 ARG cc_start: 0.7787 (tmt170) cc_final: 0.7485 (tmt170) REVERT: B 514 MET cc_start: 0.6228 (mtm) cc_final: 0.5178 (mtt) REVERT: B 519 ARG cc_start: 0.8386 (mmp80) cc_final: 0.8185 (mmp80) outliers start: 31 outliers final: 21 residues processed: 309 average time/residue: 0.0749 time to fit residues: 34.5728 Evaluate side-chains 285 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 412 HIS 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: 7.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4006 r_free = 0.4006 target = 0.154695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127877 restraints weight = 15686.782| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.54 r_work: 0.3537 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10021 Z= 0.110 Angle : 0.628 9.538 13656 Z= 0.290 Chirality : 0.043 0.199 1623 Planarity : 0.004 0.047 1672 Dihedral : 3.944 42.569 1266 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 3.25 % Allowed : 20.25 % Favored : 76.50 % 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: -1.27 (0.25), residues: 1168 helix: 0.85 (0.26), residues: 431 sheet: -2.92 (0.48), residues: 109 loop : -1.72 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.016 0.001 TYR B 349 PHE 0.015 0.001 PHE A 706 TRP 0.011 0.001 TRP B 137 HIS 0.008 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9992) covalent geometry : angle 0.62137 / 0.29 (13573) SS BOND : bond 0.00225 / 0.11 ( 4) SS BOND : angle 0.59320 / 0.35 ( 8) hydrogen bonds : bond 0.03685 / 2.51 ( 349) hydrogen bonds : angle 4.13371 / 2.77 ( 1005) link_BETA1-4 : bond 0.00391 / 0.18 ( 9) link_BETA1-4 : angle 1.19018 / 0.89 ( 27) link_NAG-ASN : bond 0.00148 / 0.06 ( 16) link_NAG-ASN : angle 1.41666 / 0.85 ( 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 309 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 ASN cc_start: 0.8100 (m-40) cc_final: 0.7687 (m110) REVERT: B 132 PHE cc_start: 0.8685 (t80) cc_final: 0.8438 (t80) REVERT: B 189 LYS cc_start: 0.8465 (mtpt) cc_final: 0.7774 (mmtm) REVERT: B 268 LEU cc_start: 0.7050 (mt) cc_final: 0.6756 (pp) REVERT: B 365 TYR cc_start: 0.8697 (m-80) cc_final: 0.8452 (m-80) REVERT: B 462 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7604 (mp0) REVERT: B 473 ILE cc_start: 0.9139 (mt) cc_final: 0.8899 (mp) REVERT: B 476 TRP cc_start: 0.9133 (t60) cc_final: 0.8550 (t60) REVERT: B 513 ARG cc_start: 0.7915 (tmt170) cc_final: 0.7580 (tmt170) REVERT: B 514 MET cc_start: 0.6289 (mtm) cc_final: 0.5366 (mtm) REVERT: B 517 LYS cc_start: 0.7413 (ptpt) cc_final: 0.7201 (ptpt) outliers start: 34 outliers final: 22 residues processed: 291 average time/residue: 0.0761 time to fit residues: 33.2428 Evaluate side-chains 277 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL 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 128 VAL Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 263 ASN 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 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: 0.8980 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3992 r_free = 0.3992 target = 0.153568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126764 restraints weight = 15723.167| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.53 r_work: 0.3517 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10021 Z= 0.109 Angle : 0.605 9.156 13656 Z= 0.282 Chirality : 0.043 0.212 1623 Planarity : 0.004 0.050 1672 Dihedral : 3.898 43.038 1265 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 3.82 % Allowed : 20.06 % Favored : 76.12 % 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: -1.02 (0.25), residues: 1168 helix: 1.09 (0.26), residues: 431 sheet: -2.82 (0.47), residues: 109 loop : -1.59 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 519 TYR 0.018 0.001 TYR B 94 PHE 0.018 0.001 PHE A 375 TRP 0.011 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9992) covalent geometry : angle 0.60071 / 0.28 (13573) SS BOND : bond 0.00241 / 0.12 ( 4) SS BOND : angle 0.54359 / 0.31 ( 8) hydrogen bonds : bond 0.03437 / 2.35 ( 349) hydrogen bonds : angle 3.97392 / 2.65 ( 1005) link_BETA1-4 : bond 0.00348 / 0.19 ( 9) link_BETA1-4 : angle 1.10493 / 0.81 ( 27) link_NAG-ASN : bond 0.00247 / 0.16 ( 16) link_NAG-ASN : angle 1.16547 / 0.70 ( 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 316 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 ASN cc_start: 0.8117 (m-40) cc_final: 0.7658 (m110) REVERT: B 132 PHE cc_start: 0.8714 (t80) cc_final: 0.8473 (t80) REVERT: B 189 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7783 (mmtm) REVERT: B 268 LEU cc_start: 0.6903 (mt) cc_final: 0.6659 (pp) REVERT: B 334 HIS cc_start: 0.9283 (m170) cc_final: 0.8789 (m-70) REVERT: B 365 TYR cc_start: 0.8729 (m-80) cc_final: 0.8391 (m-80) REVERT: B 462 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7635 (mp0) REVERT: B 473 ILE cc_start: 0.9121 (mt) cc_final: 0.8899 (mp) REVERT: B 476 TRP cc_start: 0.9163 (t60) cc_final: 0.8600 (t60) REVERT: B 513 ARG cc_start: 0.8032 (tmt170) cc_final: 0.7684 (tmt170) REVERT: B 514 MET cc_start: 0.5956 (mtm) cc_final: 0.4978 (mtm) outliers start: 40 outliers final: 25 residues processed: 298 average time/residue: 0.0712 time to fit residues: 32.3402 Evaluate side-chains 288 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 490 VAL 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 115 ILE 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 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: 1.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.153160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126591 restraints weight = 15756.728| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.46 r_work: 0.3516 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10021 Z= 0.109 Angle : 0.603 8.749 13656 Z= 0.280 Chirality : 0.043 0.247 1623 Planarity : 0.004 0.048 1672 Dihedral : 3.890 43.767 1265 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 3.63 % Allowed : 21.97 % Favored : 74.40 % 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: -0.83 (0.25), residues: 1168 helix: 1.25 (0.26), residues: 429 sheet: -2.76 (0.48), residues: 109 loop : -1.45 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 320 TYR 0.017 0.001 TYR A 383 PHE 0.015 0.001 PHE A 294 TRP 0.011 0.001 TRP B 137 HIS 0.006 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9992) covalent geometry : angle 0.59642 / 0.28 (13573) SS BOND : bond 0.00204 / 0.10 ( 4) SS BOND : angle 0.50142 / 0.28 ( 8) hydrogen bonds : bond 0.03434 / 2.37 ( 349) hydrogen bonds : angle 3.92098 / 2.60 ( 1005) link_BETA1-4 : bond 0.00348 / 0.17 ( 9) link_BETA1-4 : angle 1.11930 / 0.81 ( 27) link_NAG-ASN : bond 0.00265 / 0.18 ( 16) link_NAG-ASN : angle 1.47038 / 0.83 ( 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 305 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 MET cc_start: 0.8488 (mtp) cc_final: 0.8186 (mtp) REVERT: B 132 PHE cc_start: 0.8687 (t80) cc_final: 0.8438 (t80) REVERT: B 189 LYS cc_start: 0.8553 (mtpt) cc_final: 0.7825 (mmtm) REVERT: B 333 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8071 (mmmt) REVERT: B 365 TYR cc_start: 0.8819 (m-80) cc_final: 0.8467 (m-80) REVERT: B 462 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7701 (mp0) REVERT: B 473 ILE cc_start: 0.9116 (mt) cc_final: 0.8895 (mp) REVERT: B 476 TRP cc_start: 0.9189 (t60) cc_final: 0.8561 (t60) REVERT: B 513 ARG cc_start: 0.7961 (tmt170) cc_final: 0.7742 (tmt170) REVERT: B 514 MET cc_start: 0.6204 (mtm) cc_final: 0.5285 (mtm) outliers start: 38 outliers final: 29 residues processed: 287 average time/residue: 0.0705 time to fit residues: 30.9600 Evaluate side-chains 290 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 490 VAL Chi-restraints excluded: chain A residue 498 SER 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 79 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN 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 456 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: 3.9990 chunk 112 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 539 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.140893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114468 restraints weight = 16325.964| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.44 r_work: 0.3341 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 10021 Z= 0.338 Angle : 0.807 8.246 13656 Z= 0.394 Chirality : 0.050 0.322 1623 Planarity : 0.005 0.051 1672 Dihedral : 4.763 44.129 1265 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.98 % Rotamer: Outliers : 4.78 % Allowed : 21.78 % Favored : 73.45 % 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: -0.96 (0.25), residues: 1168 helix: 1.21 (0.27), residues: 401 sheet: -2.98 (0.46), residues: 112 loop : -1.43 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 320 TYR 0.026 0.003 TYR B 90 PHE 0.033 0.002 PHE A 702 TRP 0.022 0.002 TRP B 137 HIS 0.011 0.002 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.34 ( 9992) covalent geometry : angle 0.79887 / 0.39 (13573) SS BOND : bond 0.00479 / 0.24 ( 4) SS BOND : angle 1.27487 / 0.69 ( 8) hydrogen bonds : bond 0.04885 / 3.33 ( 349) hydrogen bonds : angle 4.41269 / 2.93 ( 1005) link_BETA1-4 : bond 0.00641 / 0.38 ( 9) link_BETA1-4 : angle 1.27959 / 0.86 ( 27) link_NAG-ASN : bond 0.00443 / 0.24 ( 16) link_NAG-ASN : angle 1.93332 / 1.14 ( 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 306 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 PHE cc_start: 0.8775 (t80) cc_final: 0.8537 (t80) REVERT: B 207 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7461 (ttp80) REVERT: B 320 ARG cc_start: 0.7678 (mmp80) cc_final: 0.6792 (mmt90) REVERT: B 332 PHE cc_start: 0.8528 (m-80) cc_final: 0.8210 (m-80) REVERT: B 333 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8136 (mmmt) REVERT: B 346 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8731 (t80) REVERT: B 462 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7919 (mp0) REVERT: B 476 TRP cc_start: 0.9306 (t60) cc_final: 0.8625 (t60) REVERT: B 513 ARG cc_start: 0.7929 (tmt170) cc_final: 0.7440 (tmt170) REVERT: B 514 MET cc_start: 0.6327 (mtm) cc_final: 0.5163 (mtt) outliers start: 50 outliers final: 32 residues processed: 282 average time/residue: 0.0735 time to fit residues: 31.5882 Evaluate side-chains 272 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 490 VAL Chi-restraints excluded: chain A residue 498 SER 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 75 TYR 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 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 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU 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 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: 0.9980 chunk 33 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119200 restraints weight = 15877.944| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.44 r_work: 0.3414 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10021 Z= 0.137 Angle : 0.686 9.247 13656 Z= 0.318 Chirality : 0.045 0.231 1623 Planarity : 0.004 0.055 1672 Dihedral : 4.401 47.734 1265 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 3.82 % Allowed : 24.26 % Favored : 71.92 % 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: -0.76 (0.26), residues: 1168 helix: 1.27 (0.26), residues: 414 sheet: -2.88 (0.48), residues: 109 loop : -1.28 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.027 0.002 TYR B 349 PHE 0.016 0.001 PHE A 294 TRP 0.013 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9992) covalent geometry : angle 0.68104 / 0.32 (13573) SS BOND : bond 0.00312 / 0.16 ( 4) SS BOND : angle 1.11749 / 0.62 ( 8) hydrogen bonds : bond 0.04113 / 2.86 ( 349) hydrogen bonds : angle 4.19573 / 2.78 ( 1005) link_BETA1-4 : bond 0.00346 / 0.17 ( 9) link_BETA1-4 : angle 1.05159 / 0.76 ( 27) link_NAG-ASN : bond 0.00194 / 0.12 ( 16) link_NAG-ASN : angle 1.33549 / 0.79 ( 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 302 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7764 (t0) cc_final: 0.7469 (t0) REVERT: A 707 MET cc_start: 0.8521 (mtp) cc_final: 0.8222 (mtp) REVERT: B 132 PHE cc_start: 0.8756 (t80) cc_final: 0.8508 (t80) REVERT: B 207 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7387 (ttp80) REVERT: B 320 ARG cc_start: 0.7621 (mmp80) cc_final: 0.6879 (mmt90) REVERT: B 346 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8325 (t80) REVERT: B 462 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7916 (mp0) REVERT: B 473 ILE cc_start: 0.9035 (mp) cc_final: 0.8769 (mp) REVERT: B 476 TRP cc_start: 0.9235 (t60) cc_final: 0.8607 (t60) REVERT: B 513 ARG cc_start: 0.7919 (tmt170) cc_final: 0.7378 (tmt170) REVERT: B 514 MET cc_start: 0.6304 (mtm) cc_final: 0.5138 (mtt) outliers start: 40 outliers final: 32 residues processed: 288 average time/residue: 0.0726 time to fit residues: 31.8763 Evaluate side-chains 278 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 122 CYS 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 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN ** A 133 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 449 ASN ** 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 = 0.3905 r_free = 0.3905 target = 0.146872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120401 restraints weight = 16018.211| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.48 r_work: 0.3427 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3178 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= 0.129 Angle : 0.680 10.280 13656 Z= 0.311 Chirality : 0.044 0.222 1623 Planarity : 0.004 0.049 1672 Dihedral : 4.256 48.252 1265 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.72 % Allowed : 24.74 % Favored : 71.54 % 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: -0.66 (0.26), residues: 1168 helix: 1.37 (0.26), residues: 414 sheet: -2.85 (0.48), residues: 109 loop : -1.23 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 519 TYR 0.019 0.001 TYR B 349 PHE 0.016 0.001 PHE A 294 TRP 0.012 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9992) covalent geometry : angle 0.67552 / 0.31 (13573) SS BOND : bond 0.00245 / 0.12 ( 4) SS BOND : angle 0.71390 / 0.38 ( 8) hydrogen bonds : bond 0.03813 / 2.64 ( 349) hydrogen bonds : angle 4.13141 / 2.75 ( 1005) link_BETA1-4 : bond 0.00341 / 0.17 ( 9) link_BETA1-4 : angle 1.07613 / 0.77 ( 27) link_NAG-ASN : bond 0.00196 / 0.11 ( 16) link_NAG-ASN : angle 1.26657 / 0.75 ( 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 299 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7767 (t0) cc_final: 0.7525 (t0) REVERT: A 328 ASN cc_start: 0.8969 (t0) cc_final: 0.8080 (t0) REVERT: A 627 LYS cc_start: 0.8818 (mttt) cc_final: 0.8563 (ttmt) REVERT: A 707 MET cc_start: 0.8528 (mtp) cc_final: 0.8252 (mtp) REVERT: A 713 LEU cc_start: 0.7863 (tp) cc_final: 0.7632 (mt) REVERT: B 207 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7561 (ttp80) REVERT: B 333 LYS cc_start: 0.8611 (mttp) cc_final: 0.8104 (mmmt) REVERT: B 346 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8335 (t80) REVERT: B 462 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7897 (mp0) REVERT: B 473 ILE cc_start: 0.9051 (mp) cc_final: 0.8778 (mp) REVERT: B 476 TRP cc_start: 0.9242 (t60) cc_final: 0.8610 (t60) REVERT: B 513 ARG cc_start: 0.7939 (tmt170) cc_final: 0.7407 (tmt170) REVERT: B 514 MET cc_start: 0.6301 (mtm) cc_final: 0.5140 (mtt) outliers start: 39 outliers final: 33 residues processed: 285 average time/residue: 0.0786 time to fit residues: 33.6447 Evaluate side-chains 286 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 66 LEU 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 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 402 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 SER 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 217 LEU Chi-restraints excluded: chain B residue 240 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 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 522 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 110 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 236 GLN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** 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 = 0.3896 r_free = 0.3896 target = 0.146117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119893 restraints weight = 15912.128| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.45 r_work: 0.3425 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3283 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= 0.139 Angle : 0.702 9.947 13656 Z= 0.319 Chirality : 0.045 0.219 1623 Planarity : 0.004 0.045 1672 Dihedral : 4.283 48.534 1265 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 3.92 % Allowed : 25.21 % Favored : 70.87 % 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: -0.59 (0.26), residues: 1168 helix: 1.43 (0.26), residues: 413 sheet: -2.82 (0.48), residues: 109 loop : -1.18 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 320 TYR 0.017 0.002 TYR A 383 PHE 0.015 0.001 PHE A 294 TRP 0.012 0.001 TRP B 137 HIS 0.007 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9992) covalent geometry : angle 0.69801 / 0.32 (13573) SS BOND : bond 0.00256 / 0.13 ( 4) SS BOND : angle 0.70412 / 0.37 ( 8) hydrogen bonds : bond 0.03801 / 2.63 ( 349) hydrogen bonds : angle 4.11436 / 2.74 ( 1005) link_BETA1-4 : bond 0.00330 / 0.15 ( 9) link_BETA1-4 : angle 1.09025 / 0.77 ( 27) link_NAG-ASN : bond 0.00192 / 0.11 ( 16) link_NAG-ASN : angle 1.28799 / 0.76 ( 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 298 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 257 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7759 (t0) cc_final: 0.7497 (t0) REVERT: A 626 GLU cc_start: 0.8242 (pt0) cc_final: 0.7601 (pp20) REVERT: A 627 LYS cc_start: 0.8843 (mttt) cc_final: 0.8352 (ttmt) REVERT: A 707 MET cc_start: 0.8525 (mtp) cc_final: 0.8237 (mtp) REVERT: A 713 LEU cc_start: 0.7826 (tp) cc_final: 0.7552 (mt) REVERT: B 207 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7705 (ttp80) REVERT: B 316 GLU cc_start: 0.8463 (tp30) cc_final: 0.8182 (tp30) REVERT: B 320 ARG cc_start: 0.7250 (mmp80) cc_final: 0.6733 (mmt90) REVERT: B 333 LYS cc_start: 0.8607 (mttp) cc_final: 0.8118 (mmmt) REVERT: B 346 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8415 (t80) REVERT: B 462 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7869 (mp0) REVERT: B 473 ILE cc_start: 0.9047 (mp) cc_final: 0.8761 (mp) REVERT: B 476 TRP cc_start: 0.9240 (t60) cc_final: 0.8604 (t60) REVERT: B 513 ARG cc_start: 0.7956 (tmt170) cc_final: 0.7432 (tmt170) REVERT: B 514 MET cc_start: 0.6276 (mtm) cc_final: 0.5031 (mtt) outliers start: 41 outliers final: 35 residues processed: 280 average time/residue: 0.0759 time to fit residues: 31.8752 Evaluate side-chains 289 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 402 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER 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 195 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 240 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 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 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** 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 = 0.3836 r_free = 0.3836 target = 0.140854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114494 restraints weight = 16124.883| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.42 r_work: 0.3365 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10021 Z= 0.266 Angle : 0.794 8.825 13656 Z= 0.374 Chirality : 0.048 0.275 1623 Planarity : 0.004 0.047 1672 Dihedral : 4.632 47.352 1265 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 4.01 % Allowed : 25.31 % Favored : 70.68 % 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: -0.73 (0.26), residues: 1168 helix: 1.32 (0.27), residues: 407 sheet: -2.90 (0.49), residues: 109 loop : -1.25 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 519 TYR 0.027 0.002 TYR B 90 PHE 0.024 0.002 PHE A 702 TRP 0.021 0.002 TRP B 137 HIS 0.007 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 ( 9992) covalent geometry : angle 0.78826 / 0.37 (13573) SS BOND : bond 0.00398 / 0.20 ( 4) SS BOND : angle 1.13963 / 0.62 ( 8) hydrogen bonds : bond 0.04433 / 3.08 ( 349) hydrogen bonds : angle 4.34067 / 2.89 ( 1005) link_BETA1-4 : bond 0.00343 / 0.16 ( 9) link_BETA1-4 : angle 1.17632 / 0.79 ( 27) link_NAG-ASN : bond 0.00306 / 0.17 ( 16) link_NAG-ASN : angle 1.64226 / 0.96 ( 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 285 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7840 (t0) cc_final: 0.7539 (t0) REVERT: A 627 LYS cc_start: 0.8926 (mttt) cc_final: 0.8607 (ttmt) REVERT: A 707 MET cc_start: 0.8540 (mtp) cc_final: 0.8252 (mtp) REVERT: B 98 LYS cc_start: 0.9474 (ttmt) cc_final: 0.9256 (ttmt) REVERT: B 207 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7741 (ttp80) REVERT: B 225 TYR cc_start: 0.8564 (m-80) cc_final: 0.8147 (m-80) REVERT: B 320 ARG cc_start: 0.7348 (mmp80) cc_final: 0.6982 (mmt90) REVERT: B 333 LYS cc_start: 0.8620 (mttp) cc_final: 0.8143 (mmmt) REVERT: B 346 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8563 (t80) REVERT: B 462 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7944 (mp0) REVERT: B 473 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 476 TRP cc_start: 0.9266 (t60) cc_final: 0.8669 (t60) REVERT: B 513 ARG cc_start: 0.7944 (tmt170) cc_final: 0.7460 (tmt170) REVERT: B 514 MET cc_start: 0.6355 (mtm) cc_final: 0.5076 (mtt) outliers start: 42 outliers final: 38 residues processed: 266 average time/residue: 0.0781 time to fit residues: 31.0705 Evaluate side-chains 281 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 147 LYS 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 402 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 518 ILE 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 217 LEU Chi-restraints excluded: chain B residue 240 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 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 412 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 ILE 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: 0.8980 chunk 95 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 4 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120442 restraints weight = 15920.547| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.48 r_work: 0.3436 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10021 Z= 0.121 Angle : 0.719 11.477 13656 Z= 0.325 Chirality : 0.045 0.205 1623 Planarity : 0.004 0.044 1672 Dihedral : 4.343 49.478 1265 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 3.34 % Allowed : 25.98 % Favored : 70.68 % 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: -0.63 (0.26), residues: 1168 helix: 1.37 (0.26), residues: 414 sheet: -2.88 (0.49), residues: 109 loop : -1.18 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 519 TYR 0.018 0.002 TYR A 383 PHE 0.049 0.001 PHE B 483 TRP 0.011 0.001 TRP A 546 HIS 0.007 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9992) covalent geometry : angle 0.71626 / 0.32 (13573) SS BOND : bond 0.00253 / 0.13 ( 4) SS BOND : angle 0.58460 / 0.30 ( 8) hydrogen bonds : bond 0.03742 / 2.60 ( 349) hydrogen bonds : angle 4.12047 / 2.74 ( 1005) link_BETA1-4 : bond 0.00367 / 0.19 ( 9) link_BETA1-4 : angle 1.05379 / 0.77 ( 27) link_NAG-ASN : bond 0.00250 / 0.14 ( 16) link_NAG-ASN : angle 1.18008 / 0.70 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.03 seconds wall clock time: 46 minutes 59.60 seconds (2819.60 seconds total)