Starting phenix.real_space_refine on Mon Jul 28 00:01:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c76_30293/07_2025/7c76_30293.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c76_30293/07_2025/7c76_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_30293/07_2025/7c76_30293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c76_30293/07_2025/7c76_30293.map" model { file = "/net/cci-nas-00/data/ceres_data/7c76_30293/07_2025/7c76_30293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c76_30293/07_2025/7c76_30293.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5563 Classifications: {'peptide': 691} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3855 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 20, 'TRANS': 462} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.30, per 1000 atoms: 0.65 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: 2.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.00 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: 3.50 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3031 1.35 - 1.46: 2472 1.46 - 1.58: 4424 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 9992 Sorted by residual: bond pdb=" C PRO B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 4.14e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 9987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 13136 1.58 - 3.15: 359 3.15 - 4.73: 53 4.73 - 6.30: 21 6.30 - 7.88: 4 Bond angle restraints: 13573 Sorted by residual: angle pdb=" C ASN A 140 " pdb=" N ASN A 141 " pdb=" CA ASN A 141 " ideal model delta sigma weight residual 121.80 129.06 -7.26 2.44e+00 1.68e-01 8.86e+00 angle pdb=" N ASN A 141 " pdb=" CA ASN A 141 " pdb=" C ASN A 141 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.03e+00 angle pdb=" CA LEU B 500 " pdb=" CB LEU B 500 " pdb=" CG LEU B 500 " ideal model delta sigma weight residual 116.30 124.18 -7.88 3.50e+00 8.16e-02 5.07e+00 angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" C PRO B 208 " ideal model delta sigma weight residual 110.70 113.31 -2.61 1.22e+00 6.72e-01 4.59e+00 angle pdb=" N THR B 126 " pdb=" CA THR B 126 " pdb=" C THR B 126 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.50e+00 ... (remaining 13568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 5628 21.75 - 43.51: 516 43.51 - 65.26: 61 65.26 - 87.01: 27 87.01 - 108.77: 11 Dihedral angle restraints: 6243 sinusoidal: 2807 harmonic: 3436 Sorted by residual: dihedral pdb=" CA PRO B 208 " pdb=" C PRO B 208 " pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 95 " pdb=" SG CYS A 95 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -48.50 -37.50 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.94 108.77 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 6240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1395 0.058 - 0.116: 212 0.116 - 0.174: 12 0.174 - 0.232: 1 0.232 - 0.290: 3 Chirality restraints: 1623 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 247 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1620 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 312 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 313 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 207 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 208 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 208 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 209 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " 0.024 5.00e-02 4.00e+02 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1208 2.76 - 3.29: 9743 3.29 - 3.83: 16679 3.83 - 4.36: 18951 4.36 - 4.90: 32613 Nonbonded interactions: 79194 Sorted by model distance: nonbonded pdb=" O HIS B 229 " pdb=" OG SER B 383 " model vdw 2.219 3.040 nonbonded pdb=" O ASP A 347 " pdb=" OG SER A 350 " model vdw 2.267 3.040 nonbonded pdb=" O LEU A 637 " pdb=" OG1 THR A 666 " model vdw 2.272 3.040 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 178 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU B 353 " pdb=" OG SER B 446 " model vdw 2.278 3.040 ... (remaining 79189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.970 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10021 Z= 0.165 Angle : 0.632 7.878 13656 Z= 0.305 Chirality : 0.043 0.290 1623 Planarity : 0.003 0.048 1672 Dihedral : 16.860 108.767 4011 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (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 TRP 0.006 0.001 TRP B 476 HIS 0.009 0.000 HIS B 475 PHE 0.013 0.001 PHE A 647 TYR 0.011 0.001 TYR B 248 ARG 0.007 0.001 ARG B 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 16) link_NAG-ASN : angle 0.97459 ( 48) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 1.15771 ( 27) hydrogen bonds : bond 0.15708 ( 349) hydrogen bonds : angle 5.94682 ( 1005) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.31183 ( 8) covalent geometry : bond 0.00324 ( 9992) covalent geometry : angle 0.62861 (13573) *********************** 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 : 1.007 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: 0.1964 time to fit residues: 94.0062 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 : 1.015 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 299 GLN A 380 ASN 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 = 0.3916 r_free = 0.3916 target = 0.147035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120584 restraints weight = 15931.651| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.44 r_work: 0.3439 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10021 Z= 0.253 Angle : 0.750 10.046 13656 Z= 0.360 Chirality : 0.048 0.327 1623 Planarity : 0.005 0.046 1672 Dihedral : 7.866 58.458 1793 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 3.53 % Allowed : 17.38 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.25), residues: 1168 helix: 0.53 (0.26), residues: 424 sheet: -3.16 (0.46), residues: 110 loop : -1.86 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 656 HIS 0.009 0.001 HIS B 89 PHE 0.020 0.002 PHE B 483 TYR 0.023 0.002 TYR B 90 ARG 0.004 0.001 ARG B 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 16) link_NAG-ASN : angle 1.52908 ( 48) link_BETA1-4 : bond 0.00406 ( 9) link_BETA1-4 : angle 1.86797 ( 27) hydrogen bonds : bond 0.04558 ( 349) hydrogen bonds : angle 4.43930 ( 1005) SS BOND : bond 0.00397 ( 4) SS BOND : angle 1.15195 ( 8) covalent geometry : bond 0.00582 ( 9992) covalent geometry : angle 0.74185 (13573) *********************** 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 319 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8434 (t0) cc_final: 0.8017 (t0) REVERT: A 626 GLU cc_start: 0.8428 (pt0) cc_final: 0.7857 (pp20) REVERT: B 132 PHE cc_start: 0.8695 (t80) cc_final: 0.8459 (t80) REVERT: B 189 LYS cc_start: 0.8567 (mtpt) cc_final: 0.7836 (mmtm) REVERT: B 334 HIS cc_start: 0.9484 (m170) cc_final: 0.9054 (m-70) REVERT: B 346 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8655 (t80) REVERT: B 365 TYR cc_start: 0.8705 (m-80) cc_final: 0.8388 (m-80) REVERT: B 462 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7835 (mp0) REVERT: B 473 ILE cc_start: 0.9169 (mt) cc_final: 0.8945 (mp) REVERT: B 476 TRP cc_start: 0.9245 (t60) cc_final: 0.8662 (t60) REVERT: B 513 ARG cc_start: 0.7884 (tmt170) cc_final: 0.7567 (tmt170) REVERT: B 514 MET cc_start: 0.6308 (mtm) cc_final: 0.5247 (mtt) outliers start: 37 outliers final: 26 residues processed: 302 average time/residue: 0.1839 time to fit residues: 81.6650 Evaluate side-chains 286 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 490 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 61 LEU 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 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 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 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 92 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122980 restraints weight = 15781.947| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.49 r_work: 0.3472 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10021 Z= 0.125 Angle : 0.647 9.697 13656 Z= 0.302 Chirality : 0.044 0.250 1623 Planarity : 0.004 0.045 1672 Dihedral : 6.311 52.301 1787 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 3.44 % Allowed : 20.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.25), residues: 1168 helix: 0.91 (0.26), residues: 428 sheet: -3.07 (0.47), residues: 110 loop : -1.70 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 137 HIS 0.009 0.001 HIS B 475 PHE 0.015 0.001 PHE A 706 TYR 0.018 0.001 TYR B 349 ARG 0.008 0.001 ARG B 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 16) link_NAG-ASN : angle 1.29549 ( 48) link_BETA1-4 : bond 0.00362 ( 9) link_BETA1-4 : angle 1.62779 ( 27) hydrogen bonds : bond 0.03955 ( 349) hydrogen bonds : angle 4.16022 ( 1005) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.73550 ( 8) covalent geometry : bond 0.00285 ( 9992) covalent geometry : angle 0.64008 (13573) *********************** 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 311 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8356 (t0) cc_final: 0.7898 (t0) REVERT: A 626 GLU cc_start: 0.8244 (pt0) cc_final: 0.8017 (mt-10) REVERT: B 98 LYS cc_start: 0.9392 (ttmt) cc_final: 0.8961 (ttpt) REVERT: B 132 PHE cc_start: 0.8788 (t80) cc_final: 0.8541 (t80) REVERT: B 189 LYS cc_start: 0.8545 (mtpt) cc_final: 0.7825 (mmtm) REVERT: B 334 HIS cc_start: 0.9480 (m170) cc_final: 0.9044 (m-70) REVERT: B 365 TYR cc_start: 0.8712 (m-80) cc_final: 0.8372 (m-80) REVERT: B 462 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7740 (mp0) REVERT: B 476 TRP cc_start: 0.9168 (t60) cc_final: 0.8534 (t60) REVERT: B 513 ARG cc_start: 0.7940 (tmt170) cc_final: 0.7718 (tmt170) REVERT: B 514 MET cc_start: 0.6323 (mtm) cc_final: 0.5506 (mtm) REVERT: B 519 ARG cc_start: 0.8230 (mmp80) cc_final: 0.7798 (tpp-160) outliers start: 36 outliers final: 22 residues processed: 294 average time/residue: 0.1928 time to fit residues: 85.0645 Evaluate side-chains 284 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 128 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 373 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 109 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 334 HIS ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.143917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117736 restraints weight = 16008.841| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.38 r_work: 0.3388 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10021 Z= 0.223 Angle : 0.688 8.214 13656 Z= 0.332 Chirality : 0.046 0.300 1623 Planarity : 0.004 0.052 1672 Dihedral : 5.795 53.638 1786 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.18 % Rotamer: Outliers : 5.44 % Allowed : 21.78 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 1168 helix: 1.10 (0.27), residues: 417 sheet: -3.03 (0.48), residues: 110 loop : -1.52 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 137 HIS 0.007 0.001 HIS A 724 PHE 0.020 0.002 PHE A 702 TYR 0.022 0.002 TYR B 90 ARG 0.004 0.001 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 16) link_NAG-ASN : angle 1.47834 ( 48) link_BETA1-4 : bond 0.00350 ( 9) link_BETA1-4 : angle 1.46504 ( 27) hydrogen bonds : bond 0.04341 ( 349) hydrogen bonds : angle 4.23358 ( 1005) SS BOND : bond 0.00408 ( 4) SS BOND : angle 0.94601 ( 8) covalent geometry : bond 0.00518 ( 9992) covalent geometry : angle 0.68056 (13573) *********************** 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 312 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8382 (t0) cc_final: 0.7903 (t0) REVERT: A 656 TRP cc_start: 0.8531 (t60) cc_final: 0.8290 (t60) REVERT: A 721 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8077 (mt) REVERT: B 132 PHE cc_start: 0.8759 (t80) cc_final: 0.8487 (t80) REVERT: B 207 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7420 (ttp80) REVERT: B 334 HIS cc_start: 0.9248 (OUTLIER) cc_final: 0.8994 (m-70) REVERT: B 337 ASP cc_start: 0.8030 (t0) cc_final: 0.7667 (t0) REVERT: B 346 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8717 (t80) REVERT: B 462 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7855 (mp0) REVERT: B 473 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8931 (mp) REVERT: B 476 TRP cc_start: 0.9292 (t60) cc_final: 0.8710 (t60) outliers start: 57 outliers final: 36 residues processed: 286 average time/residue: 0.1991 time to fit residues: 86.4757 Evaluate side-chains 285 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 A residue 600 THR Chi-restraints excluded: chain A residue 702 PHE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 106 ASP 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 236 GLN 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 302 LEU Chi-restraints excluded: chain B residue 334 HIS 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 380 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 500 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 107 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 111 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN B 244 ASN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119850 restraints weight = 15809.698| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.48 r_work: 0.3419 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10021 Z= 0.125 Angle : 0.631 8.792 13656 Z= 0.298 Chirality : 0.044 0.262 1623 Planarity : 0.004 0.053 1672 Dihedral : 5.480 53.003 1786 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 4.30 % Allowed : 23.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1168 helix: 1.31 (0.27), residues: 411 sheet: -2.90 (0.49), residues: 110 loop : -1.41 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 137 HIS 0.017 0.001 HIS B 334 PHE 0.017 0.001 PHE A 630 TYR 0.019 0.001 TYR B 349 ARG 0.007 0.000 ARG B 513 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 16) link_NAG-ASN : angle 1.19795 ( 48) link_BETA1-4 : bond 0.00327 ( 9) link_BETA1-4 : angle 1.27369 ( 27) hydrogen bonds : bond 0.03884 ( 349) hydrogen bonds : angle 4.07393 ( 1005) SS BOND : bond 0.00260 ( 4) SS BOND : angle 0.92444 ( 8) covalent geometry : bond 0.00289 ( 9992) covalent geometry : angle 0.62609 (13573) *********************** 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 304 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8476 (t0) cc_final: 0.8129 (t0) REVERT: A 707 MET cc_start: 0.8477 (mtp) cc_final: 0.8185 (mtp) REVERT: B 98 LYS cc_start: 0.9397 (ttmt) cc_final: 0.8957 (ttpt) REVERT: B 132 PHE cc_start: 0.8815 (t80) cc_final: 0.8576 (t80) REVERT: B 207 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7477 (ttp80) REVERT: B 333 LYS cc_start: 0.8668 (mttp) cc_final: 0.8357 (mttt) REVERT: B 378 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8773 (tt) REVERT: B 462 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7911 (mp0) REVERT: B 473 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8972 (mp) REVERT: B 476 TRP cc_start: 0.9222 (t60) cc_final: 0.8584 (t60) outliers start: 45 outliers final: 34 residues processed: 283 average time/residue: 0.2527 time to fit residues: 106.1364 Evaluate side-chains 285 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 501 LEU 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 61 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118317 restraints weight = 16079.753| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.45 r_work: 0.3395 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10021 Z= 0.164 Angle : 0.650 8.319 13656 Z= 0.309 Chirality : 0.045 0.284 1623 Planarity : 0.004 0.049 1672 Dihedral : 5.441 53.417 1786 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 4.78 % Allowed : 24.93 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1168 helix: 1.40 (0.27), residues: 411 sheet: -2.85 (0.50), residues: 109 loop : -1.38 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 137 HIS 0.007 0.001 HIS B 412 PHE 0.016 0.002 PHE A 630 TYR 0.019 0.002 TYR B 349 ARG 0.008 0.001 ARG B 519 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 16) link_NAG-ASN : angle 1.32349 ( 48) link_BETA1-4 : bond 0.00350 ( 9) link_BETA1-4 : angle 1.23409 ( 27) hydrogen bonds : bond 0.03974 ( 349) hydrogen bonds : angle 4.10240 ( 1005) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.83640 ( 8) covalent geometry : bond 0.00381 ( 9992) covalent geometry : angle 0.64482 (13573) *********************** 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 : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7777 (t0) cc_final: 0.7453 (t0) REVERT: A 364 ASP cc_start: 0.8516 (t0) cc_final: 0.7966 (t0) REVERT: A 615 LEU cc_start: 0.8652 (tp) cc_final: 0.8275 (mp) REVERT: A 707 MET cc_start: 0.8480 (mtp) cc_final: 0.8186 (mtp) REVERT: B 132 PHE cc_start: 0.8781 (t80) cc_final: 0.8536 (t80) REVERT: B 207 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7569 (ttp80) REVERT: B 320 ARG cc_start: 0.7499 (mmp80) cc_final: 0.6887 (mmp80) REVERT: B 333 LYS cc_start: 0.8744 (mttp) cc_final: 0.8396 (mttt) REVERT: B 346 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8625 (t80) REVERT: B 378 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8753 (tt) REVERT: B 462 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7962 (mp0) REVERT: B 473 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8942 (mp) REVERT: B 476 TRP cc_start: 0.9236 (t60) cc_final: 0.8676 (t60) REVERT: B 519 ARG cc_start: 0.8127 (mmp80) cc_final: 0.7884 (tpp-160) outliers start: 50 outliers final: 35 residues processed: 286 average time/residue: 0.1756 time to fit residues: 74.5960 Evaluate side-chains 291 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 A residue 650 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 497 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 63 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3860 r_free = 0.3860 target = 0.143942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117053 restraints weight = 15972.277| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.70 r_work: 0.3379 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3112 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= 0.117 Angle : 0.633 9.807 13656 Z= 0.294 Chirality : 0.044 0.255 1623 Planarity : 0.004 0.045 1672 Dihedral : 5.212 53.084 1786 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 4.58 % Allowed : 25.69 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1168 helix: 1.49 (0.27), residues: 411 sheet: -2.66 (0.51), residues: 108 loop : -1.29 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.006 0.001 HIS B 475 PHE 0.019 0.001 PHE B 483 TYR 0.019 0.001 TYR B 349 ARG 0.005 0.000 ARG B 519 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 16) link_NAG-ASN : angle 1.16300 ( 48) link_BETA1-4 : bond 0.00371 ( 9) link_BETA1-4 : angle 1.19014 ( 27) hydrogen bonds : bond 0.03686 ( 349) hydrogen bonds : angle 3.99638 ( 1005) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.61230 ( 8) covalent geometry : bond 0.00271 ( 9992) covalent geometry : angle 0.62911 (13573) *********************** 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 311 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7761 (t0) cc_final: 0.7463 (t0) REVERT: A 364 ASP cc_start: 0.8434 (t0) cc_final: 0.8066 (t0) REVERT: A 433 LEU cc_start: 0.8764 (tp) cc_final: 0.8502 (tp) REVERT: A 457 ASN cc_start: 0.8029 (m-40) cc_final: 0.7377 (p0) REVERT: A 615 LEU cc_start: 0.8653 (tp) cc_final: 0.8294 (mp) REVERT: A 707 MET cc_start: 0.8516 (mtp) cc_final: 0.8217 (mtp) REVERT: B 139 MET cc_start: 0.8541 (mtp) cc_final: 0.8338 (mtp) REVERT: B 207 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7649 (ttp80) REVERT: B 239 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8121 (ttt) REVERT: B 333 LYS cc_start: 0.8726 (mttp) cc_final: 0.8370 (mttt) REVERT: B 337 ASP cc_start: 0.7806 (t0) cc_final: 0.7467 (t0) REVERT: B 346 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8540 (t80) REVERT: B 378 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8714 (tt) REVERT: B 462 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7908 (mp0) REVERT: B 473 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8913 (mp) REVERT: B 476 TRP cc_start: 0.9192 (t60) cc_final: 0.8575 (t60) outliers start: 48 outliers final: 39 residues processed: 287 average time/residue: 0.1824 time to fit residues: 77.9393 Evaluate side-chains 296 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 306 GLU 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 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 A residue 650 THR 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 236 GLN Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 497 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 108 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117205 restraints weight = 16035.806| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.69 r_work: 0.3373 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3176 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= 0.127 Angle : 0.647 9.181 13656 Z= 0.301 Chirality : 0.044 0.261 1623 Planarity : 0.004 0.045 1672 Dihedral : 5.131 53.385 1786 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 4.68 % Allowed : 25.79 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1168 helix: 1.44 (0.26), residues: 411 sheet: -2.64 (0.51), residues: 108 loop : -1.24 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 137 HIS 0.006 0.001 HIS B 475 PHE 0.018 0.001 PHE B 483 TYR 0.018 0.001 TYR B 349 ARG 0.010 0.000 ARG B 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 16) link_NAG-ASN : angle 1.19932 ( 48) link_BETA1-4 : bond 0.00357 ( 9) link_BETA1-4 : angle 1.19786 ( 27) hydrogen bonds : bond 0.03719 ( 349) hydrogen bonds : angle 4.00893 ( 1005) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.64003 ( 8) covalent geometry : bond 0.00295 ( 9992) covalent geometry : angle 0.64270 (13573) *********************** 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 306 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7770 (t0) cc_final: 0.7472 (t0) REVERT: A 364 ASP cc_start: 0.8444 (t0) cc_final: 0.8060 (t0) REVERT: A 433 LEU cc_start: 0.8757 (tp) cc_final: 0.8496 (tp) REVERT: A 457 ASN cc_start: 0.8030 (m-40) cc_final: 0.7306 (p0) REVERT: A 615 LEU cc_start: 0.8659 (tp) cc_final: 0.8287 (mp) REVERT: A 626 GLU cc_start: 0.8275 (pt0) cc_final: 0.7710 (pp20) REVERT: A 627 LYS cc_start: 0.8779 (mttt) cc_final: 0.8266 (ttmt) REVERT: A 707 MET cc_start: 0.8505 (mtp) cc_final: 0.8201 (mtp) REVERT: B 123 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7408 (tp) REVERT: B 207 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7656 (ttp80) REVERT: B 239 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8120 (ttt) REVERT: B 316 GLU cc_start: 0.8433 (tp30) cc_final: 0.8120 (tp30) REVERT: B 319 LEU cc_start: 0.8070 (mt) cc_final: 0.7768 (mp) REVERT: B 320 ARG cc_start: 0.7246 (mmp80) cc_final: 0.6704 (mmt90) REVERT: B 337 ASP cc_start: 0.7824 (t0) cc_final: 0.7480 (t0) REVERT: B 346 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8544 (t80) REVERT: B 462 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7813 (mp0) REVERT: B 473 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8886 (mp) REVERT: B 476 TRP cc_start: 0.9193 (t60) cc_final: 0.8472 (t60) outliers start: 49 outliers final: 40 residues processed: 281 average time/residue: 0.2037 time to fit residues: 84.3346 Evaluate side-chains 299 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 306 GLU 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 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 A residue 650 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 497 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 106 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115364 restraints weight = 16502.110| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.40 r_work: 0.3367 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10021 Z= 0.204 Angle : 0.713 11.754 13656 Z= 0.336 Chirality : 0.046 0.292 1623 Planarity : 0.004 0.048 1672 Dihedral : 5.419 54.439 1786 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 5.06 % Allowed : 26.17 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1168 helix: 1.40 (0.27), residues: 406 sheet: -2.72 (0.51), residues: 109 loop : -1.27 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 137 HIS 0.010 0.001 HIS B 412 PHE 0.018 0.002 PHE A 702 TYR 0.034 0.002 TYR B 349 ARG 0.003 0.000 ARG B 519 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 16) link_NAG-ASN : angle 1.41993 ( 48) link_BETA1-4 : bond 0.00325 ( 9) link_BETA1-4 : angle 1.21937 ( 27) hydrogen bonds : bond 0.04257 ( 349) hydrogen bonds : angle 4.15363 ( 1005) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.97379 ( 8) covalent geometry : bond 0.00478 ( 9992) covalent geometry : angle 0.70817 (13573) *********************** 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 302 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7871 (t0) cc_final: 0.7605 (t0) REVERT: A 364 ASP cc_start: 0.8667 (t0) cc_final: 0.8099 (t0) REVERT: A 615 LEU cc_start: 0.8874 (tp) cc_final: 0.8505 (mp) REVERT: A 707 MET cc_start: 0.8531 (mtp) cc_final: 0.8229 (mtp) REVERT: B 207 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7643 (ttp80) REVERT: B 239 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8195 (ttt) REVERT: B 320 ARG cc_start: 0.7447 (mmp80) cc_final: 0.6997 (mmt90) REVERT: B 337 ASP cc_start: 0.8058 (t0) cc_final: 0.7757 (t0) REVERT: B 346 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8636 (t80) REVERT: B 462 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7930 (mp0) REVERT: B 473 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8973 (mp) REVERT: B 476 TRP cc_start: 0.9281 (t60) cc_final: 0.8709 (t60) outliers start: 53 outliers final: 37 residues processed: 280 average time/residue: 0.1715 time to fit residues: 71.8294 Evaluate side-chains 288 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 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 A residue 650 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 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 236 GLN Chi-restraints excluded: chain B residue 239 MET 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 380 VAL 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 500 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN B 334 HIS ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113413 restraints weight = 16624.074| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.37 r_work: 0.3338 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10021 Z= 0.258 Angle : 0.764 10.601 13656 Z= 0.363 Chirality : 0.048 0.305 1623 Planarity : 0.004 0.049 1672 Dihedral : 5.744 55.136 1786 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 4.68 % Allowed : 27.03 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1168 helix: 1.32 (0.26), residues: 405 sheet: -2.85 (0.51), residues: 109 loop : -1.39 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 137 HIS 0.011 0.001 HIS B 412 PHE 0.021 0.002 PHE A 702 TYR 0.027 0.002 TYR B 349 ARG 0.006 0.001 ARG B 519 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 16) link_NAG-ASN : angle 1.51790 ( 48) link_BETA1-4 : bond 0.00358 ( 9) link_BETA1-4 : angle 1.23276 ( 27) hydrogen bonds : bond 0.04456 ( 349) hydrogen bonds : angle 4.29951 ( 1005) SS BOND : bond 0.00388 ( 4) SS BOND : angle 1.16214 ( 8) covalent geometry : bond 0.00600 ( 9992) covalent geometry : angle 0.75830 (13573) ********************** 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 298 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7777 (t0) cc_final: 0.7485 (t0) REVERT: A 364 ASP cc_start: 0.8692 (t0) cc_final: 0.8135 (t0) REVERT: A 707 MET cc_start: 0.8535 (mtp) cc_final: 0.8252 (mtp) REVERT: A 723 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8668 (mm) REVERT: B 179 MET cc_start: 0.8813 (tpp) cc_final: 0.7937 (mmm) REVERT: B 207 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7668 (ttp80) REVERT: B 239 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (ttt) REVERT: B 320 ARG cc_start: 0.7521 (mmp80) cc_final: 0.7065 (mmt90) REVERT: B 333 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8105 (mmmt) REVERT: B 337 ASP cc_start: 0.8075 (t0) cc_final: 0.7831 (t0) REVERT: B 346 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8657 (t80) REVERT: B 462 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7979 (mp0) REVERT: B 473 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8979 (mp) REVERT: B 476 TRP cc_start: 0.9289 (t60) cc_final: 0.8699 (t60) outliers start: 49 outliers final: 40 residues processed: 277 average time/residue: 0.2085 time to fit residues: 85.9039 Evaluate side-chains 290 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 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 236 GLN Chi-restraints excluded: chain B residue 239 MET 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 378 LEU Chi-restraints excluded: chain B residue 380 VAL 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 487 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 92 optimal weight: 0.0980 chunk 113 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3890 r_free = 0.3890 target = 0.144292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118150 restraints weight = 16277.334| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.42 r_work: 0.3404 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10021 Z= 0.126 Angle : 0.715 11.153 13656 Z= 0.326 Chirality : 0.045 0.251 1623 Planarity : 0.004 0.047 1672 Dihedral : 5.403 54.156 1786 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 3.63 % Allowed : 28.56 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1168 helix: 1.43 (0.27), residues: 406 sheet: -2.79 (0.51), residues: 109 loop : -1.26 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 137 HIS 0.008 0.001 HIS B 412 PHE 0.046 0.002 PHE B 483 TYR 0.023 0.002 TYR B 349 ARG 0.008 0.001 ARG B 519 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 16) link_NAG-ASN : angle 1.22572 ( 48) link_BETA1-4 : bond 0.00364 ( 9) link_BETA1-4 : angle 1.17878 ( 27) hydrogen bonds : bond 0.03934 ( 349) hydrogen bonds : angle 4.12237 ( 1005) SS BOND : bond 0.00274 ( 4) SS BOND : angle 0.67940 ( 8) covalent geometry : bond 0.00289 ( 9992) covalent geometry : angle 0.71104 (13573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6737.04 seconds wall clock time: 119 minutes 54.96 seconds (7194.96 seconds total)