Starting phenix.real_space_refine on Wed Mar 4 04:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q49_13799/03_2026/7q49_13799_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q49_13799/03_2026/7q49_13799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q49_13799/03_2026/7q49_13799_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q49_13799/03_2026/7q49_13799_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q49_13799/03_2026/7q49_13799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q49_13799/03_2026/7q49_13799.map" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.059 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 19 5.16 5 C 3398 2.51 5 N 873 2.21 5 O 1045 1.98 5 H 4788 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10124 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 9804 Classifications: {'peptide': 616} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 577} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" 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: "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: 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: "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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.16, per 1000 atoms: 0.21 Number of scatterers: 10124 At special positions: 0 Unit cell: (77.38, 89.04, 93.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 19 16.00 O 1045 8.00 N 873 7.00 C 3398 6.00 H 4788 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " BETA1-6 " NAG C 1 " - " FUC C 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1302 " - " ASN A 82 " " NAG A1303 " - " ASN A 416 " " NAG B 1 " - " ASN A 25 " " NAG C 1 " - " ASN A 289 " " NAG D 1 " - " ASN A 9 " " NAG E 1 " - " ASN A 117 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 480 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 336.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 365 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 361 " 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 70.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.804A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 removed outlier: 3.758A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.583A pdb=" N ALA A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 190 Proline residue: A 170 - end of helix Proline residue: A 173 - end of helix removed outlier: 3.644A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.803A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 279 through 286 removed outlier: 3.578A pdb=" N GLN A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.620A pdb=" N ARG A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.966A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 373 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.590A pdb=" N GLY A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 452 removed outlier: 4.473A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.557A pdb=" N TRP A 463 " --> pdb=" O TYR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.682A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.526A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.065A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 336 294 hydrogen bonds defined for protein. 843 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: 2.24 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4787 1.04 - 1.24: 587 1.24 - 1.44: 1914 1.44 - 1.63: 2960 1.63 - 1.83: 31 Bond restraints: 10279 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.358 0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.463 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG E 2 " pdb=" C2 NAG E 2 " ideal model delta sigma weight residual 1.532 1.491 0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.366 0.040 2.00e-02 2.50e+03 3.95e+00 ... (remaining 10274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17208 1.59 - 3.17: 956 3.17 - 4.76: 158 4.76 - 6.35: 29 6.35 - 7.93: 9 Bond angle restraints: 18360 Sorted by residual: angle pdb=" C LYS A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta sigma weight residual 121.62 115.31 6.31 1.83e+00 2.99e-01 1.19e+01 angle pdb=" N LYS A 321 " pdb=" CA LYS A 321 " pdb=" C LYS A 321 " ideal model delta sigma weight residual 109.81 102.50 7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" CA TYR A 338 " pdb=" CB TYR A 338 " pdb=" CG TYR A 338 " ideal model delta sigma weight residual 113.90 108.25 5.65 1.80e+00 3.09e-01 9.85e+00 angle pdb=" N THR A 349 " pdb=" CA THR A 349 " pdb=" C THR A 349 " ideal model delta sigma weight residual 110.23 114.52 -4.29 1.45e+00 4.76e-01 8.77e+00 angle pdb=" N PHE A 83 " pdb=" CA PHE A 83 " pdb=" CB PHE A 83 " ideal model delta sigma weight residual 109.48 113.98 -4.50 1.55e+00 4.16e-01 8.42e+00 ... (remaining 18355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 4789 21.35 - 42.69: 288 42.69 - 64.04: 98 64.04 - 85.39: 49 85.39 - 106.73: 29 Dihedral angle restraints: 5253 sinusoidal: 2996 harmonic: 2257 Sorted by residual: dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.02 106.73 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.53 105.15 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.74 104.45 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 5250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 682 0.066 - 0.132: 146 0.132 - 0.198: 14 0.198 - 0.264: 5 0.264 - 0.330: 7 Chirality restraints: 854 Sorted by residual: 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 -2.60 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 851 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 508 " -0.046 2.00e-02 2.50e+03 5.32e-02 4.25e+01 pdb=" CD GLN A 508 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN A 508 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 GLN A 508 " 0.077 2.00e-02 2.50e+03 pdb="HE21 GLN A 508 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN A 508 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 479 " -0.130 9.50e-02 1.11e+02 5.15e-02 1.91e+01 pdb=" NE ARG A 479 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 479 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 479 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG A 479 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 479 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 479 " 0.045 2.00e-02 2.50e+03 pdb="HH21 ARG A 479 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 479 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 371 " 0.028 2.00e-02 2.50e+03 3.34e-02 1.67e+01 pdb=" CD GLN A 371 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN A 371 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 371 " -0.051 2.00e-02 2.50e+03 pdb="HE21 GLN A 371 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 371 " 0.050 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 309 2.14 - 2.76: 18476 2.76 - 3.37: 28899 3.37 - 3.99: 35865 3.99 - 4.60: 56711 Nonbonded interactions: 140260 Sorted by model distance: nonbonded pdb=" HG1 THR A 454 " pdb=" OD2 ASP A 462 " model vdw 1.526 2.450 nonbonded pdb=" HG1 THR A 468 " pdb=" O ILE A 473 " model vdw 1.531 2.450 nonbonded pdb=" HH TYR A 521 " pdb=" O PRO A 524 " model vdw 1.558 2.450 nonbonded pdb=" O TRP A 40 " pdb=" HG1 THR A 44 " model vdw 1.559 2.450 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.594 2.450 ... (remaining 140255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.430 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: 0.050 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.008 0.048 5521 Z= 0.383 Angle : 1.149 12.193 7565 Z= 0.582 Chirality : 0.061 0.330 854 Planarity : 0.009 0.105 935 Dihedral : 19.174 106.734 2370 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.19 % Allowed : 1.70 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.30), residues: 614 helix: -0.60 (0.22), residues: 367 sheet: -0.97 (1.76), residues: 10 loop : -1.48 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.005 ARG A 479 TYR 0.032 0.005 TYR A 338 PHE 0.028 0.004 PHE A 509 TRP 0.052 0.006 TRP A 257 HIS 0.010 0.003 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00829 ( 5491) covalent geometry : angle 1.08126 ( 7484) SS BOND : bond 0.00321 ( 3) SS BOND : angle 2.13321 ( 6) hydrogen bonds : bond 0.24029 ( 294) hydrogen bonds : angle 8.35387 ( 843) metal coordination : bond 0.00936 ( 2) link_ALPHA1-3 : bond 0.00376 ( 2) link_ALPHA1-3 : angle 3.15416 ( 6) link_ALPHA1-6 : bond 0.00820 ( 2) link_ALPHA1-6 : angle 1.40444 ( 6) link_BETA1-4 : bond 0.00557 ( 12) link_BETA1-4 : angle 3.37957 ( 36) link_BETA1-6 : bond 0.00342 ( 1) link_BETA1-6 : angle 1.24911 ( 3) link_NAG-ASN : bond 0.00977 ( 8) link_NAG-ASN : angle 5.50364 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8231 (pt0) cc_final: 0.8019 (tt0) REVERT: A 52 ARG cc_start: 0.8909 (tpt170) cc_final: 0.8677 (ttp-110) REVERT: A 132 LYS cc_start: 0.8260 (tttt) cc_final: 0.7988 (mmmt) REVERT: A 155 MET cc_start: 0.8060 (tpt) cc_final: 0.7768 (tpt) REVERT: A 156 LEU cc_start: 0.9086 (tp) cc_final: 0.8766 (tp) REVERT: A 182 SER cc_start: 0.9198 (t) cc_final: 0.8766 (m) REVERT: A 183 ASN cc_start: 0.8342 (m-40) cc_final: 0.8080 (t0) REVERT: A 215 TYR cc_start: 0.7170 (t80) cc_final: 0.6800 (t80) REVERT: A 219 GLU cc_start: 0.7979 (tt0) cc_final: 0.7645 (mt-10) REVERT: A 298 GLU cc_start: 0.8454 (tt0) cc_final: 0.7973 (tm-30) REVERT: A 302 THR cc_start: 0.9124 (p) cc_final: 0.8427 (p) REVERT: A 341 LYS cc_start: 0.7998 (mttt) cc_final: 0.7674 (mmpt) REVERT: A 347 GLN cc_start: 0.7883 (tp-100) cc_final: 0.7658 (tp40) REVERT: A 350 ARG cc_start: 0.7662 (ttt180) cc_final: 0.7384 (ttm170) REVERT: A 453 ARG cc_start: 0.7352 (mtt90) cc_final: 0.6909 (tmm160) REVERT: A 579 GLN cc_start: 0.7818 (tt0) cc_final: 0.7450 (tm-30) REVERT: A 592 LEU cc_start: 0.8423 (mt) cc_final: 0.8163 (pt) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.2215 time to fit residues: 33.7517 Evaluate side-chains 80 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 292 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN A 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095847 restraints weight = 27271.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100803 restraints weight = 10501.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103897 restraints weight = 5365.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105917 restraints weight = 3307.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107276 restraints weight = 2328.184| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5521 Z= 0.184 Angle : 0.832 10.466 7565 Z= 0.419 Chirality : 0.044 0.207 854 Planarity : 0.005 0.046 935 Dihedral : 13.869 69.905 1180 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.51 % Allowed : 8.49 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.32), residues: 614 helix: 0.55 (0.25), residues: 379 sheet: None (None), residues: 0 loop : -0.71 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.019 0.002 TYR A 372 PHE 0.021 0.002 PHE A 387 TRP 0.018 0.002 TRP A 552 HIS 0.010 0.002 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 5491) covalent geometry : angle 0.79603 ( 7484) SS BOND : bond 0.00288 ( 3) SS BOND : angle 3.36043 ( 6) hydrogen bonds : bond 0.07979 ( 294) hydrogen bonds : angle 5.65512 ( 843) metal coordination : bond 0.00265 ( 2) link_ALPHA1-3 : bond 0.00483 ( 2) link_ALPHA1-3 : angle 2.52575 ( 6) link_ALPHA1-6 : bond 0.00284 ( 2) link_ALPHA1-6 : angle 1.72608 ( 6) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 2.55560 ( 36) link_BETA1-6 : bond 0.00156 ( 1) link_BETA1-6 : angle 1.40780 ( 3) link_NAG-ASN : bond 0.00304 ( 8) link_NAG-ASN : angle 2.36356 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8892 (tpt170) cc_final: 0.8658 (ttp-110) REVERT: A 132 LYS cc_start: 0.8145 (tttt) cc_final: 0.7906 (mmmt) REVERT: A 161 GLU cc_start: 0.8262 (tt0) cc_final: 0.8040 (tm-30) REVERT: A 182 SER cc_start: 0.9111 (t) cc_final: 0.8709 (m) REVERT: A 183 ASN cc_start: 0.8285 (m-40) cc_final: 0.7942 (t0) REVERT: A 215 TYR cc_start: 0.6780 (t80) cc_final: 0.6259 (t80) REVERT: A 283 MET cc_start: 0.8585 (ttp) cc_final: 0.8369 (ttp) REVERT: A 350 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7249 (ttm170) REVERT: A 379 LEU cc_start: 0.8050 (mt) cc_final: 0.7754 (mt) REVERT: A 384 ASN cc_start: 0.7333 (p0) cc_final: 0.6962 (p0) REVERT: A 453 ARG cc_start: 0.7283 (mtt90) cc_final: 0.6862 (tmm160) REVERT: A 462 ASP cc_start: 0.8036 (m-30) cc_final: 0.7167 (t0) REVERT: A 582 GLN cc_start: 0.7846 (mt0) cc_final: 0.7392 (tp40) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.2060 time to fit residues: 26.3359 Evaluate side-chains 86 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 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 = 0.3655 r_free = 0.3655 target = 0.116244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095839 restraints weight = 28164.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.100544 restraints weight = 11111.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103536 restraints weight = 5859.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105488 restraints weight = 3726.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106658 restraints weight = 2698.348| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5521 Z= 0.163 Angle : 0.713 6.431 7565 Z= 0.354 Chirality : 0.041 0.188 854 Planarity : 0.005 0.056 935 Dihedral : 10.296 61.276 1180 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.32 % Allowed : 11.13 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.33), residues: 614 helix: 0.93 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.19 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.021 0.002 TYR A 372 PHE 0.014 0.002 PHE A 158 TRP 0.014 0.001 TRP A 552 HIS 0.012 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5491) covalent geometry : angle 0.68402 ( 7484) SS BOND : bond 0.00442 ( 3) SS BOND : angle 1.43371 ( 6) hydrogen bonds : bond 0.06538 ( 294) hydrogen bonds : angle 5.21201 ( 843) metal coordination : bond 0.00115 ( 2) link_ALPHA1-3 : bond 0.00941 ( 2) link_ALPHA1-3 : angle 1.96389 ( 6) link_ALPHA1-6 : bond 0.00435 ( 2) link_ALPHA1-6 : angle 1.60496 ( 6) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 2.35318 ( 36) link_BETA1-6 : bond 0.00353 ( 1) link_BETA1-6 : angle 1.26500 ( 3) link_NAG-ASN : bond 0.00321 ( 8) link_NAG-ASN : angle 1.92631 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6606 (tt) REVERT: A 182 SER cc_start: 0.9132 (t) cc_final: 0.8879 (m) REVERT: A 183 ASN cc_start: 0.8373 (m-40) cc_final: 0.8165 (t0) REVERT: A 309 MET cc_start: 0.9035 (mmp) cc_final: 0.8807 (mmp) REVERT: A 379 LEU cc_start: 0.8180 (mt) cc_final: 0.7907 (mt) REVERT: A 453 ARG cc_start: 0.7405 (mtt90) cc_final: 0.7097 (tmm160) REVERT: A 462 ASP cc_start: 0.8141 (m-30) cc_final: 0.7337 (t0) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.2159 time to fit residues: 24.8695 Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.095551 restraints weight = 28260.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.100241 restraints weight = 11197.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103191 restraints weight = 5919.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105139 restraints weight = 3777.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106414 restraints weight = 2722.625| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5521 Z= 0.162 Angle : 0.663 5.577 7565 Z= 0.333 Chirality : 0.039 0.181 854 Planarity : 0.005 0.058 935 Dihedral : 8.436 59.782 1180 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.26 % Allowed : 12.26 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.34), residues: 614 helix: 1.08 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.01 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.034 0.002 TYR A 372 PHE 0.012 0.001 PHE A 509 TRP 0.014 0.001 TRP A 163 HIS 0.009 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5491) covalent geometry : angle 0.63703 ( 7484) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.92842 ( 6) hydrogen bonds : bond 0.05718 ( 294) hydrogen bonds : angle 4.99514 ( 843) metal coordination : bond 0.00123 ( 2) link_ALPHA1-3 : bond 0.00994 ( 2) link_ALPHA1-3 : angle 2.27173 ( 6) link_ALPHA1-6 : bond 0.00512 ( 2) link_ALPHA1-6 : angle 1.57417 ( 6) link_BETA1-4 : bond 0.00330 ( 12) link_BETA1-4 : angle 2.14697 ( 36) link_BETA1-6 : bond 0.00406 ( 1) link_BETA1-6 : angle 1.31288 ( 3) link_NAG-ASN : bond 0.00289 ( 8) link_NAG-ASN : angle 1.67430 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9074 (tp) cc_final: 0.8762 (tp) REVERT: A 182 SER cc_start: 0.9138 (t) cc_final: 0.8889 (m) REVERT: A 183 ASN cc_start: 0.8417 (m-40) cc_final: 0.8210 (t0) REVERT: A 215 TYR cc_start: 0.7095 (t80) cc_final: 0.6815 (t80) REVERT: A 309 MET cc_start: 0.9018 (mmp) cc_final: 0.8740 (mmp) REVERT: A 338 TYR cc_start: 0.9150 (m-80) cc_final: 0.8942 (m-10) REVERT: A 341 LYS cc_start: 0.7712 (mttt) cc_final: 0.7454 (mmpt) REVERT: A 453 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7036 (tmm160) REVERT: A 462 ASP cc_start: 0.8088 (m-30) cc_final: 0.7355 (t0) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 0.2058 time to fit residues: 23.5209 Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 549 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 GLN ** 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 = 0.3659 r_free = 0.3659 target = 0.116368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095804 restraints weight = 28236.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100481 restraints weight = 11198.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103495 restraints weight = 5949.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105464 restraints weight = 3808.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106806 restraints weight = 2763.455| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5521 Z= 0.144 Angle : 0.630 6.714 7565 Z= 0.316 Chirality : 0.038 0.191 854 Planarity : 0.004 0.050 935 Dihedral : 7.679 59.999 1180 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 12.83 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.34), residues: 614 helix: 1.14 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.06 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 550 TYR 0.015 0.001 TYR A 372 PHE 0.016 0.001 PHE A 509 TRP 0.013 0.001 TRP A 552 HIS 0.010 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5491) covalent geometry : angle 0.60791 ( 7484) SS BOND : bond 0.00305 ( 3) SS BOND : angle 1.30269 ( 6) hydrogen bonds : bond 0.05406 ( 294) hydrogen bonds : angle 4.82568 ( 843) metal coordination : bond 0.00137 ( 2) link_ALPHA1-3 : bond 0.00978 ( 2) link_ALPHA1-3 : angle 2.03638 ( 6) link_ALPHA1-6 : bond 0.00586 ( 2) link_ALPHA1-6 : angle 1.52634 ( 6) link_BETA1-4 : bond 0.00239 ( 12) link_BETA1-4 : angle 1.88618 ( 36) link_BETA1-6 : bond 0.00438 ( 1) link_BETA1-6 : angle 1.24715 ( 3) link_NAG-ASN : bond 0.00258 ( 8) link_NAG-ASN : angle 1.50697 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 SER cc_start: 0.9105 (t) cc_final: 0.8860 (m) REVERT: A 183 ASN cc_start: 0.8430 (m-40) cc_final: 0.8201 (t0) REVERT: A 215 TYR cc_start: 0.7023 (t80) cc_final: 0.6762 (t80) REVERT: A 338 TYR cc_start: 0.9158 (m-80) cc_final: 0.8956 (m-10) REVERT: A 341 LYS cc_start: 0.7730 (mttt) cc_final: 0.7465 (mmpt) REVERT: A 380 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6805 (mtp180) REVERT: A 453 ARG cc_start: 0.7401 (mtt90) cc_final: 0.7016 (tmm160) REVERT: A 462 ASP cc_start: 0.8129 (m-30) cc_final: 0.7892 (t70) outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.2008 time to fit residues: 20.6618 Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 549 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 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 545 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095881 restraints weight = 28596.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100620 restraints weight = 11225.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103662 restraints weight = 5930.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105654 restraints weight = 3790.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.106996 restraints weight = 2743.448| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5521 Z= 0.143 Angle : 0.598 5.367 7565 Z= 0.300 Chirality : 0.037 0.187 854 Planarity : 0.004 0.048 935 Dihedral : 7.091 59.175 1180 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.51 % Allowed : 13.77 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.34), residues: 614 helix: 1.30 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.13 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.012 0.001 TYR A 215 PHE 0.017 0.001 PHE A 509 TRP 0.011 0.001 TRP A 552 HIS 0.009 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5491) covalent geometry : angle 0.57772 ( 7484) SS BOND : bond 0.00570 ( 3) SS BOND : angle 1.06712 ( 6) hydrogen bonds : bond 0.05020 ( 294) hydrogen bonds : angle 4.69933 ( 843) metal coordination : bond 0.00138 ( 2) link_ALPHA1-3 : bond 0.01032 ( 2) link_ALPHA1-3 : angle 2.05688 ( 6) link_ALPHA1-6 : bond 0.00646 ( 2) link_ALPHA1-6 : angle 1.47086 ( 6) link_BETA1-4 : bond 0.00290 ( 12) link_BETA1-4 : angle 1.74819 ( 36) link_BETA1-6 : bond 0.00465 ( 1) link_BETA1-6 : angle 1.27358 ( 3) link_NAG-ASN : bond 0.00323 ( 8) link_NAG-ASN : angle 1.45526 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 SER cc_start: 0.9125 (t) cc_final: 0.8900 (m) REVERT: A 183 ASN cc_start: 0.8437 (m-40) cc_final: 0.8233 (t0) REVERT: A 215 TYR cc_start: 0.6985 (t80) cc_final: 0.6717 (t80) REVERT: A 338 TYR cc_start: 0.9183 (m-80) cc_final: 0.8949 (m-10) REVERT: A 341 LYS cc_start: 0.7759 (mttt) cc_final: 0.7482 (mmpt) REVERT: A 380 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6749 (mtp180) REVERT: A 453 ARG cc_start: 0.7283 (mtt90) cc_final: 0.6771 (tmm160) REVERT: A 599 TRP cc_start: 0.8151 (t60) cc_final: 0.7642 (t60) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.1821 time to fit residues: 19.2791 Evaluate side-chains 78 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.0870 chunk 55 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 0.0030 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.117926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097008 restraints weight = 27957.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101784 restraints weight = 11074.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104906 restraints weight = 5868.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.106903 restraints weight = 3728.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108194 restraints weight = 2705.917| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5521 Z= 0.116 Angle : 0.576 5.919 7565 Z= 0.286 Chirality : 0.037 0.196 854 Planarity : 0.004 0.045 935 Dihedral : 6.680 59.684 1180 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.51 % Allowed : 13.58 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.35), residues: 614 helix: 1.49 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.08 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 479 TYR 0.012 0.001 TYR A 175 PHE 0.022 0.001 PHE A 511 TRP 0.011 0.001 TRP A 552 HIS 0.009 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5491) covalent geometry : angle 0.55813 ( 7484) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.75896 ( 6) hydrogen bonds : bond 0.04781 ( 294) hydrogen bonds : angle 4.57432 ( 843) metal coordination : bond 0.00089 ( 2) link_ALPHA1-3 : bond 0.01019 ( 2) link_ALPHA1-3 : angle 1.93207 ( 6) link_ALPHA1-6 : bond 0.00681 ( 2) link_ALPHA1-6 : angle 1.42527 ( 6) link_BETA1-4 : bond 0.00268 ( 12) link_BETA1-4 : angle 1.65202 ( 36) link_BETA1-6 : bond 0.00527 ( 1) link_BETA1-6 : angle 1.23381 ( 3) link_NAG-ASN : bond 0.00192 ( 8) link_NAG-ASN : angle 1.27463 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9051 (tp) cc_final: 0.8747 (tp) REVERT: A 182 SER cc_start: 0.9107 (t) cc_final: 0.8876 (m) REVERT: A 341 LYS cc_start: 0.7738 (mttt) cc_final: 0.7445 (mmpt) REVERT: A 380 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6574 (mtp180) REVERT: A 453 ARG cc_start: 0.7307 (mtt90) cc_final: 0.6662 (tmm160) REVERT: A 529 ASP cc_start: 0.8549 (p0) cc_final: 0.7516 (p0) REVERT: A 582 GLN cc_start: 0.8113 (mt0) cc_final: 0.7607 (tp40) REVERT: A 599 TRP cc_start: 0.8155 (t60) cc_final: 0.7653 (t60) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.1901 time to fit residues: 19.3226 Evaluate side-chains 80 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 347 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.117080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096158 restraints weight = 28158.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100921 restraints weight = 11294.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104023 restraints weight = 6048.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106061 restraints weight = 3870.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107397 restraints weight = 2800.048| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5521 Z= 0.149 Angle : 0.591 6.053 7565 Z= 0.296 Chirality : 0.037 0.181 854 Planarity : 0.004 0.045 935 Dihedral : 6.578 59.426 1180 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.89 % Allowed : 13.58 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.35), residues: 614 helix: 1.50 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.16 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.012 0.001 TYR A 215 PHE 0.015 0.001 PHE A 509 TRP 0.010 0.001 TRP A 552 HIS 0.008 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5491) covalent geometry : angle 0.57218 ( 7484) SS BOND : bond 0.00336 ( 3) SS BOND : angle 0.88494 ( 6) hydrogen bonds : bond 0.04714 ( 294) hydrogen bonds : angle 4.60984 ( 843) metal coordination : bond 0.00142 ( 2) link_ALPHA1-3 : bond 0.00999 ( 2) link_ALPHA1-3 : angle 1.95410 ( 6) link_ALPHA1-6 : bond 0.00645 ( 2) link_ALPHA1-6 : angle 1.42511 ( 6) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 1.65424 ( 36) link_BETA1-6 : bond 0.00460 ( 1) link_BETA1-6 : angle 1.31985 ( 3) link_NAG-ASN : bond 0.00324 ( 8) link_NAG-ASN : angle 1.41221 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.7935 (tt0) cc_final: 0.7732 (tp40) REVERT: A 215 TYR cc_start: 0.6969 (t80) cc_final: 0.6684 (t80) REVERT: A 341 LYS cc_start: 0.7759 (mttt) cc_final: 0.7470 (mmpt) REVERT: A 380 ARG cc_start: 0.7113 (mtp180) cc_final: 0.6662 (mtp180) REVERT: A 453 ARG cc_start: 0.7357 (mtt90) cc_final: 0.6708 (tmm160) REVERT: A 582 GLN cc_start: 0.8141 (mt0) cc_final: 0.7626 (tp40) REVERT: A 599 TRP cc_start: 0.8198 (t60) cc_final: 0.7643 (t60) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.1710 time to fit residues: 16.8206 Evaluate side-chains 79 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** 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 = 0.3566 r_free = 0.3566 target = 0.114901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.093878 restraints weight = 28534.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099041 restraints weight = 10803.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102360 restraints weight = 5593.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104445 restraints weight = 3484.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105867 restraints weight = 2487.397| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5521 Z= 0.126 Angle : 0.563 5.206 7565 Z= 0.284 Chirality : 0.036 0.192 854 Planarity : 0.004 0.044 935 Dihedral : 6.319 59.797 1180 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 13.77 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.35), residues: 614 helix: 1.58 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.13 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.010 0.001 TYR A 215 PHE 0.016 0.001 PHE A 511 TRP 0.010 0.001 TRP A 552 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5491) covalent geometry : angle 0.54621 ( 7484) SS BOND : bond 0.00324 ( 3) SS BOND : angle 0.80293 ( 6) hydrogen bonds : bond 0.04557 ( 294) hydrogen bonds : angle 4.50645 ( 843) metal coordination : bond 0.00119 ( 2) link_ALPHA1-3 : bond 0.00890 ( 2) link_ALPHA1-3 : angle 1.79660 ( 6) link_ALPHA1-6 : bond 0.00655 ( 2) link_ALPHA1-6 : angle 1.37774 ( 6) link_BETA1-4 : bond 0.00269 ( 12) link_BETA1-4 : angle 1.58455 ( 36) link_BETA1-6 : bond 0.00503 ( 1) link_BETA1-6 : angle 1.25092 ( 3) link_NAG-ASN : bond 0.00205 ( 8) link_NAG-ASN : angle 1.27356 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.7883 (tt0) cc_final: 0.7613 (tp40) REVERT: A 156 LEU cc_start: 0.8890 (tp) cc_final: 0.8579 (tp) REVERT: A 341 LYS cc_start: 0.7798 (mttt) cc_final: 0.7449 (mmpt) REVERT: A 380 ARG cc_start: 0.6713 (mtp180) cc_final: 0.6240 (mtp180) REVERT: A 453 ARG cc_start: 0.7292 (mtt90) cc_final: 0.6534 (tmm160) REVERT: A 582 GLN cc_start: 0.7882 (mt0) cc_final: 0.7349 (tp40) REVERT: A 599 TRP cc_start: 0.8207 (t60) cc_final: 0.7517 (t60) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.1678 time to fit residues: 16.3207 Evaluate side-chains 77 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** 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 = 0.3576 r_free = 0.3576 target = 0.115683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094568 restraints weight = 28294.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099775 restraints weight = 10774.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103075 restraints weight = 5576.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105218 restraints weight = 3490.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106674 restraints weight = 2475.802| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5521 Z= 0.115 Angle : 0.557 5.992 7565 Z= 0.280 Chirality : 0.036 0.196 854 Planarity : 0.004 0.043 935 Dihedral : 6.138 59.573 1180 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.51 % Allowed : 14.34 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.35), residues: 614 helix: 1.65 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.17 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 500 TYR 0.010 0.001 TYR A 372 PHE 0.015 0.001 PHE A 511 TRP 0.011 0.001 TRP A 552 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5491) covalent geometry : angle 0.54021 ( 7484) SS BOND : bond 0.00266 ( 3) SS BOND : angle 0.75551 ( 6) hydrogen bonds : bond 0.04448 ( 294) hydrogen bonds : angle 4.45591 ( 843) metal coordination : bond 0.00094 ( 2) link_ALPHA1-3 : bond 0.00920 ( 2) link_ALPHA1-3 : angle 1.76937 ( 6) link_ALPHA1-6 : bond 0.00641 ( 2) link_ALPHA1-6 : angle 1.38115 ( 6) link_BETA1-4 : bond 0.00263 ( 12) link_BETA1-4 : angle 1.54525 ( 36) link_BETA1-6 : bond 0.00505 ( 1) link_BETA1-6 : angle 1.24818 ( 3) link_NAG-ASN : bond 0.00183 ( 8) link_NAG-ASN : angle 1.22386 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.7905 (tt0) cc_final: 0.7630 (tp40) REVERT: A 219 GLU cc_start: 0.7221 (tt0) cc_final: 0.6716 (mm-30) REVERT: A 341 LYS cc_start: 0.7760 (mttt) cc_final: 0.7422 (mmpt) REVERT: A 380 ARG cc_start: 0.6737 (mtp180) cc_final: 0.6289 (mtp180) REVERT: A 453 ARG cc_start: 0.7285 (mtt90) cc_final: 0.6515 (tmm160) REVERT: A 582 GLN cc_start: 0.7883 (mt0) cc_final: 0.7312 (tp40) REVERT: A 599 TRP cc_start: 0.8177 (t60) cc_final: 0.7491 (t60) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.1707 time to fit residues: 15.9605 Evaluate side-chains 77 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 59 optimal weight: 0.0010 chunk 13 optimal weight: 1.9990 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 GLN ** 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 = 0.3593 r_free = 0.3593 target = 0.116920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095772 restraints weight = 28513.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101052 restraints weight = 10790.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104445 restraints weight = 5553.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106629 restraints weight = 3438.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108108 restraints weight = 2430.889| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5521 Z= 0.109 Angle : 0.535 6.450 7565 Z= 0.270 Chirality : 0.035 0.196 854 Planarity : 0.004 0.042 935 Dihedral : 5.699 57.791 1180 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.32 % Allowed : 14.72 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.35), residues: 614 helix: 1.80 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.17 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.010 0.001 TYR A 372 PHE 0.014 0.001 PHE A 511 TRP 0.011 0.001 TRP A 80 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 5491) covalent geometry : angle 0.51941 ( 7484) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.68794 ( 6) hydrogen bonds : bond 0.04224 ( 294) hydrogen bonds : angle 4.34323 ( 843) metal coordination : bond 0.00063 ( 2) link_ALPHA1-3 : bond 0.00845 ( 2) link_ALPHA1-3 : angle 1.63138 ( 6) link_ALPHA1-6 : bond 0.00649 ( 2) link_ALPHA1-6 : angle 1.37881 ( 6) link_BETA1-4 : bond 0.00271 ( 12) link_BETA1-4 : angle 1.47065 ( 36) link_BETA1-6 : bond 0.00471 ( 1) link_BETA1-6 : angle 1.23928 ( 3) link_NAG-ASN : bond 0.00180 ( 8) link_NAG-ASN : angle 1.15729 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.67 seconds wall clock time: 35 minutes 46.36 seconds (2146.36 seconds total)