Starting phenix.real_space_refine on Wed Sep 17 06:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipb_60768/09_2025/9ipb_60768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipb_60768/09_2025/9ipb_60768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ipb_60768/09_2025/9ipb_60768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipb_60768/09_2025/9ipb_60768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ipb_60768/09_2025/9ipb_60768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipb_60768/09_2025/9ipb_60768.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 3776 2.51 5 N 1048 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6051 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4180 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 24, 'TRANS': 514} Chain breaks: 4 Chain: "D" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 13, 'TRANS': 216} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.37, per 1000 atoms: 0.23 Number of scatterers: 6051 At special positions: 0 Unit cell: (67.768, 106.38, 125.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1169 8.00 N 1048 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.02 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.04 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.02 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 593 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 337 " " NAG A 702 " - " ASN A 504 " " NAG B 1 " - " ASN A 328 " " NAG C 1 " - " ASN A 420 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 294.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1410 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 17 sheets defined 11.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.890A pdb=" N ILE A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.695A pdb=" N SER A 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 4.122A pdb=" N PHE A 321 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 removed outlier: 4.225A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.742A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.664A pdb=" N GLU A 397 " --> pdb=" O HIS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.057A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.938A pdb=" N TYR D 148 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 207 removed outlier: 4.080A pdb=" N THR D 207 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 342 removed outlier: 3.605A pdb=" N VAL D 342 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.684A pdb=" N LEU A 41 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ALA A 68 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 43 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN A 70 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR A 45 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 93 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ARG A 125 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 95 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N SER A 127 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 97 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 295 Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.266A pdb=" N LEU A 345 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE A 412 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 438 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 414 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER A 440 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 416 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AB1, first strand: chain 'A' and resid 524 through 526 Processing sheet with id=AB2, first strand: chain 'A' and resid 566 through 567 removed outlier: 7.167A pdb=" N ILE A 562 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N LEU A 595 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS A 585 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA A 573 " --> pdb=" O LYS A 585 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 119 through 122 Processing sheet with id=AB4, first strand: chain 'D' and resid 119 through 122 Processing sheet with id=AB5, first strand: chain 'D' and resid 126 through 128 removed outlier: 6.929A pdb=" N GLU D 126 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AB7, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AB8, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.473A pdb=" N TRP D 294 " --> pdb=" O LEU D 306 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1979 1.34 - 1.46: 1173 1.46 - 1.58: 2950 1.58 - 1.70: 0 1.70 - 1.83: 73 Bond restraints: 6175 Sorted by residual: bond pdb=" N ILE A 75 " pdb=" CA ILE A 75 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.60e-03 1.73e+04 1.92e+01 bond pdb=" N VAL A 568 " pdb=" CA VAL A 568 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N ILE A 401 " pdb=" CA ILE A 401 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.18e-02 7.18e+03 1.12e+01 bond pdb=" N VAL A 299 " pdb=" CA VAL A 299 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N VAL A 268 " pdb=" CA VAL A 268 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.76e+00 ... (remaining 6170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 7167 1.45 - 2.89: 922 2.89 - 4.34: 226 4.34 - 5.79: 38 5.79 - 7.24: 3 Bond angle restraints: 8356 Sorted by residual: angle pdb=" N HIS A 334 " pdb=" CA HIS A 334 " pdb=" C HIS A 334 " ideal model delta sigma weight residual 113.18 106.21 6.97 1.21e+00 6.83e-01 3.32e+01 angle pdb=" CA ILE A 332 " pdb=" C ILE A 332 " pdb=" O ILE A 332 " ideal model delta sigma weight residual 121.58 116.83 4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N GLU A 258 " pdb=" CA GLU A 258 " pdb=" C GLU A 258 " ideal model delta sigma weight residual 113.01 107.39 5.62 1.20e+00 6.94e-01 2.19e+01 angle pdb=" CA HIS A 566 " pdb=" C HIS A 566 " pdb=" O HIS A 566 " ideal model delta sigma weight residual 120.36 115.66 4.70 1.07e+00 8.73e-01 1.93e+01 angle pdb=" N SER A 413 " pdb=" CA SER A 413 " pdb=" C SER A 413 " ideal model delta sigma weight residual 113.50 108.70 4.80 1.23e+00 6.61e-01 1.52e+01 ... (remaining 8351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 3240 16.59 - 33.18: 424 33.18 - 49.77: 126 49.77 - 66.36: 44 66.36 - 82.95: 7 Dihedral angle restraints: 3841 sinusoidal: 1642 harmonic: 2199 Sorted by residual: dihedral pdb=" CB CYS A 486 " pdb=" SG CYS A 486 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual -86.00 -139.37 53.37 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual -86.00 -33.41 -52.59 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 338 " pdb=" CB CYS A 338 " ideal model delta sinusoidal sigma weight residual 93.00 143.08 -50.08 1 1.00e+01 1.00e-02 3.44e+01 ... (remaining 3838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 776 0.098 - 0.197: 138 0.197 - 0.295: 16 0.295 - 0.393: 1 0.393 - 0.492: 1 Chirality restraints: 932 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA ILE A 432 " pdb=" N ILE A 432 " pdb=" C ILE A 432 " pdb=" CB ILE A 432 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA VAL A 416 " pdb=" N VAL A 416 " pdb=" C VAL A 416 " pdb=" CB VAL A 416 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 929 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " -0.263 9.50e-02 1.11e+02 1.18e-01 8.75e+00 pdb=" NE ARG A 141 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.266 9.50e-02 1.11e+02 1.19e-01 8.73e+00 pdb=" NE ARG A 74 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 566 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C HIS A 566 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS A 566 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS A 567 " -0.017 2.00e-02 2.50e+03 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 2 2.20 - 2.88: 2329 2.88 - 3.55: 8522 3.55 - 4.23: 15448 4.23 - 4.90: 26136 Nonbonded interactions: 52437 Sorted by model distance: nonbonded pdb=" NH1 ARG A 114 " pdb=" OE1 GLU A 181 " model vdw 1.528 3.120 nonbonded pdb=" NH1 ARG A 114 " pdb=" CD GLU A 181 " model vdw 2.196 3.350 nonbonded pdb=" O SER A 529 " pdb=" OG SER A 529 " model vdw 2.250 3.040 nonbonded pdb=" O SER A 468 " pdb=" OG SER A 468 " model vdw 2.291 3.040 nonbonded pdb=" NE2 HIS A 359 " pdb=" O GLY D 350 " model vdw 2.337 3.120 ... (remaining 52432 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 0.040 6200 Z= 0.591 Angle : 1.070 7.235 8412 Z= 0.747 Chirality : 0.073 0.492 932 Planarity : 0.008 0.119 1080 Dihedral : 16.445 82.952 2374 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.29 % Allowed : 25.11 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.97 (0.31), residues: 755 helix: -0.70 (0.98), residues: 20 sheet: -2.04 (0.41), residues: 139 loop : -1.21 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 141 TYR 0.025 0.002 TYR D 308 PHE 0.015 0.001 PHE D 145 TRP 0.017 0.002 TRP A 453 HIS 0.002 0.000 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00800 ( 6175) covalent geometry : angle 1.06196 ( 8356) SS BOND : bond 0.00419 ( 19) SS BOND : angle 1.30593 ( 38) hydrogen bonds : bond 0.25338 ( 120) hydrogen bonds : angle 9.93395 ( 285) link_BETA1-4 : bond 0.00467 ( 2) link_BETA1-4 : angle 1.62752 ( 6) link_NAG-ASN : bond 0.00908 ( 4) link_NAG-ASN : angle 3.16040 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.235 Fit side-chains REVERT: A 31 PHE cc_start: 0.7432 (m-80) cc_final: 0.7196 (m-80) REVERT: A 125 ARG cc_start: 0.7532 (ttt180) cc_final: 0.7011 (tpt-90) REVERT: A 295 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: A 300 ARG cc_start: 0.6907 (ptp-170) cc_final: 0.6680 (ttm110) REVERT: A 455 LYS cc_start: 0.7354 (ttpp) cc_final: 0.7093 (ttpp) REVERT: A 561 TYR cc_start: 0.6851 (m-80) cc_final: 0.6186 (m-80) REVERT: D 333 LYS cc_start: 0.7239 (tptt) cc_final: 0.6465 (mtmp) outliers start: 22 outliers final: 6 residues processed: 109 average time/residue: 0.4618 time to fit residues: 53.1367 Evaluate side-chains 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 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 139 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN D 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.209591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158683 restraints weight = 6310.296| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.47 r_work: 0.3787 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6200 Z= 0.184 Angle : 0.640 9.178 8412 Z= 0.326 Chirality : 0.050 0.527 932 Planarity : 0.005 0.037 1080 Dihedral : 7.406 111.346 964 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.58 % Allowed : 23.02 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.69 (0.31), residues: 755 helix: 0.19 (1.00), residues: 20 sheet: -1.92 (0.42), residues: 138 loop : -1.02 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 84 TYR 0.024 0.002 TYR D 308 PHE 0.023 0.002 PHE D 220 TRP 0.011 0.002 TRP D 163 HIS 0.009 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 6175) covalent geometry : angle 0.62033 ( 8356) SS BOND : bond 0.00489 ( 19) SS BOND : angle 1.24917 ( 38) hydrogen bonds : bond 0.04461 ( 120) hydrogen bonds : angle 7.17167 ( 285) link_BETA1-4 : bond 0.00304 ( 2) link_BETA1-4 : angle 1.63594 ( 6) link_NAG-ASN : bond 0.00532 ( 4) link_NAG-ASN : angle 3.57108 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 23 HIS cc_start: 0.3608 (OUTLIER) cc_final: 0.3319 (m170) REVERT: A 35 GLU cc_start: 0.7727 (tt0) cc_final: 0.6878 (tm-30) REVERT: A 60 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 125 ARG cc_start: 0.7450 (ttt180) cc_final: 0.6333 (tpt-90) REVERT: A 370 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7398 (mp) REVERT: A 388 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: A 455 LYS cc_start: 0.7226 (ttpp) cc_final: 0.6547 (ttpp) REVERT: A 483 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.5554 (m170) REVERT: A 524 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.5934 (mm-30) REVERT: A 535 HIS cc_start: 0.7738 (t-90) cc_final: 0.7437 (t-90) REVERT: A 537 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 561 TYR cc_start: 0.6785 (m-80) cc_final: 0.6162 (m-80) REVERT: D 263 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6918 (tp) REVERT: D 333 LYS cc_start: 0.6682 (tptt) cc_final: 0.5735 (mtmm) outliers start: 44 outliers final: 17 residues processed: 121 average time/residue: 0.4422 time to fit residues: 56.6505 Evaluate side-chains 106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.0370 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.0020 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 384 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.211163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.160484 restraints weight = 6308.781| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.47 r_work: 0.3824 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6200 Z= 0.137 Angle : 0.591 7.728 8412 Z= 0.300 Chirality : 0.049 0.587 932 Planarity : 0.004 0.036 1080 Dihedral : 5.927 44.686 959 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.83 % Allowed : 24.81 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.56 (0.31), residues: 755 helix: 0.43 (1.08), residues: 20 sheet: -1.85 (0.44), residues: 132 loop : -0.94 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.017 0.001 TYR D 308 PHE 0.015 0.002 PHE A 31 TRP 0.009 0.001 TRP D 163 HIS 0.008 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6175) covalent geometry : angle 0.56926 ( 8356) SS BOND : bond 0.00356 ( 19) SS BOND : angle 1.13748 ( 38) hydrogen bonds : bond 0.03588 ( 120) hydrogen bonds : angle 6.64403 ( 285) link_BETA1-4 : bond 0.00255 ( 2) link_BETA1-4 : angle 1.61038 ( 6) link_NAG-ASN : bond 0.00902 ( 4) link_NAG-ASN : angle 3.71811 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6969 (tmtt) cc_final: 0.6597 (tmtt) REVERT: A 23 HIS cc_start: 0.3599 (OUTLIER) cc_final: 0.3261 (m170) REVERT: A 35 GLU cc_start: 0.7710 (tt0) cc_final: 0.6918 (tm-30) REVERT: A 60 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: A 114 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6793 (ttp-170) REVERT: A 125 ARG cc_start: 0.7410 (ttt180) cc_final: 0.6287 (tpt-90) REVERT: A 294 MET cc_start: 0.6655 (tpt) cc_final: 0.6397 (tpt) REVERT: A 295 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: A 370 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 388 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: A 446 CYS cc_start: 0.5731 (OUTLIER) cc_final: 0.5484 (t) REVERT: A 455 LYS cc_start: 0.7218 (ttpp) cc_final: 0.6545 (ttpp) REVERT: A 535 HIS cc_start: 0.7745 (t-90) cc_final: 0.7515 (t-90) REVERT: A 537 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6399 (mm-30) REVERT: A 561 TYR cc_start: 0.6779 (m-80) cc_final: 0.6129 (m-80) REVERT: D 263 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6912 (tp) REVERT: D 333 LYS cc_start: 0.6644 (tptt) cc_final: 0.5698 (mtmp) outliers start: 39 outliers final: 15 residues processed: 111 average time/residue: 0.4913 time to fit residues: 57.5279 Evaluate side-chains 106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** D 359 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 = 0.4387 r_free = 0.4387 target = 0.209631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158364 restraints weight = 6361.912| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.50 r_work: 0.3805 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6200 Z= 0.163 Angle : 0.597 7.872 8412 Z= 0.300 Chirality : 0.048 0.545 932 Planarity : 0.004 0.043 1080 Dihedral : 5.995 45.570 959 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.98 % Allowed : 25.26 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.53 (0.31), residues: 755 helix: 0.40 (1.10), residues: 20 sheet: -1.69 (0.44), residues: 132 loop : -0.95 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.021 0.001 TYR D 308 PHE 0.014 0.002 PHE D 220 TRP 0.010 0.001 TRP D 163 HIS 0.008 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6175) covalent geometry : angle 0.57471 ( 8356) SS BOND : bond 0.00410 ( 19) SS BOND : angle 1.16923 ( 38) hydrogen bonds : bond 0.03356 ( 120) hydrogen bonds : angle 6.41683 ( 285) link_BETA1-4 : bond 0.00263 ( 2) link_BETA1-4 : angle 1.71213 ( 6) link_NAG-ASN : bond 0.00904 ( 4) link_NAG-ASN : angle 3.77797 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6917 (tmtt) cc_final: 0.6528 (tmtt) REVERT: A 23 HIS cc_start: 0.3522 (OUTLIER) cc_final: 0.3153 (m170) REVERT: A 35 GLU cc_start: 0.7669 (tt0) cc_final: 0.6798 (tm-30) REVERT: A 60 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: A 125 ARG cc_start: 0.7379 (ttt180) cc_final: 0.6146 (tpt-90) REVERT: A 370 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7262 (mp) REVERT: A 388 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: A 446 CYS cc_start: 0.5680 (OUTLIER) cc_final: 0.5434 (t) REVERT: A 455 LYS cc_start: 0.7126 (ttpp) cc_final: 0.6406 (ttpp) REVERT: A 535 HIS cc_start: 0.7724 (t-90) cc_final: 0.7483 (t-90) REVERT: A 537 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 561 TYR cc_start: 0.6777 (m-80) cc_final: 0.6029 (m-80) REVERT: D 263 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6820 (mp) REVERT: D 278 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6298 (mmm160) REVERT: D 333 LYS cc_start: 0.6506 (tptt) cc_final: 0.5549 (mtmp) outliers start: 40 outliers final: 17 residues processed: 116 average time/residue: 0.5087 time to fit residues: 62.2100 Evaluate side-chains 108 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.210399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159794 restraints weight = 6426.247| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.48 r_work: 0.3818 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6200 Z= 0.137 Angle : 0.577 8.068 8412 Z= 0.290 Chirality : 0.049 0.589 932 Planarity : 0.004 0.043 1080 Dihedral : 5.873 44.067 957 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.83 % Allowed : 26.31 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.48 (0.31), residues: 755 helix: 0.38 (1.11), residues: 20 sheet: -1.63 (0.44), residues: 132 loop : -0.92 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.017 0.001 TYR D 308 PHE 0.016 0.002 PHE A 54 TRP 0.009 0.001 TRP D 163 HIS 0.007 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6175) covalent geometry : angle 0.55426 ( 8356) SS BOND : bond 0.00340 ( 19) SS BOND : angle 1.11615 ( 38) hydrogen bonds : bond 0.03017 ( 120) hydrogen bonds : angle 6.14055 ( 285) link_BETA1-4 : bond 0.00212 ( 2) link_BETA1-4 : angle 1.65952 ( 6) link_NAG-ASN : bond 0.00821 ( 4) link_NAG-ASN : angle 3.72002 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6916 (tmtt) cc_final: 0.6534 (tmtt) REVERT: A 23 HIS cc_start: 0.3534 (OUTLIER) cc_final: 0.3137 (m170) REVERT: A 35 GLU cc_start: 0.7639 (tt0) cc_final: 0.6813 (tm-30) REVERT: A 60 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: A 125 ARG cc_start: 0.7350 (ttt180) cc_final: 0.6148 (tpt-90) REVERT: A 295 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: A 309 CYS cc_start: 0.5296 (OUTLIER) cc_final: 0.5049 (t) REVERT: A 331 ASN cc_start: 0.7020 (m-40) cc_final: 0.6613 (m110) REVERT: A 367 GLU cc_start: 0.7366 (mp0) cc_final: 0.6962 (mp0) REVERT: A 370 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7234 (mp) REVERT: A 388 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: A 400 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: A 446 CYS cc_start: 0.5740 (OUTLIER) cc_final: 0.5489 (t) REVERT: A 455 LYS cc_start: 0.7110 (ttpp) cc_final: 0.6395 (ttpp) REVERT: A 535 HIS cc_start: 0.7682 (t-90) cc_final: 0.7451 (t-90) REVERT: A 561 TYR cc_start: 0.6771 (m-80) cc_final: 0.5943 (m-80) REVERT: D 119 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: D 263 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6841 (mp) REVERT: D 333 LYS cc_start: 0.6488 (tptt) cc_final: 0.5542 (mtmp) outliers start: 39 outliers final: 16 residues processed: 114 average time/residue: 0.5582 time to fit residues: 66.7597 Evaluate side-chains 106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 384 GLN A 469 ASN ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.207578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156905 restraints weight = 6324.829| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.44 r_work: 0.3760 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6200 Z= 0.191 Angle : 0.619 8.601 8412 Z= 0.308 Chirality : 0.050 0.587 932 Planarity : 0.004 0.040 1080 Dihedral : 6.090 46.879 957 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.28 % Allowed : 26.16 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.61 (0.31), residues: 755 helix: 0.30 (1.11), residues: 20 sheet: -1.84 (0.43), residues: 139 loop : -0.97 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 278 TYR 0.026 0.002 TYR D 308 PHE 0.016 0.002 PHE D 220 TRP 0.011 0.002 TRP D 163 HIS 0.007 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6175) covalent geometry : angle 0.59568 ( 8356) SS BOND : bond 0.00569 ( 19) SS BOND : angle 1.35954 ( 38) hydrogen bonds : bond 0.03191 ( 120) hydrogen bonds : angle 6.19759 ( 285) link_BETA1-4 : bond 0.00315 ( 2) link_BETA1-4 : angle 1.80772 ( 6) link_NAG-ASN : bond 0.00983 ( 4) link_NAG-ASN : angle 3.77115 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7061 (tmtt) cc_final: 0.6708 (tmtt) REVERT: A 23 HIS cc_start: 0.3565 (OUTLIER) cc_final: 0.3078 (m170) REVERT: A 35 GLU cc_start: 0.7748 (tt0) cc_final: 0.6992 (tm-30) REVERT: A 125 ARG cc_start: 0.7458 (ttt180) cc_final: 0.6347 (tpt-90) REVERT: A 134 ASN cc_start: 0.5870 (OUTLIER) cc_final: 0.5615 (t0) REVERT: A 188 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.5587 (tppt) REVERT: A 295 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: A 367 GLU cc_start: 0.7444 (mp0) cc_final: 0.7093 (mp0) REVERT: A 370 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7393 (mp) REVERT: A 388 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: A 400 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 446 CYS cc_start: 0.5862 (OUTLIER) cc_final: 0.5612 (t) REVERT: A 455 LYS cc_start: 0.7254 (ttpp) cc_final: 0.6533 (ttpp) REVERT: A 524 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: A 535 HIS cc_start: 0.7738 (t-90) cc_final: 0.7525 (t-90) REVERT: A 561 TYR cc_start: 0.6824 (m-80) cc_final: 0.5983 (m-80) REVERT: D 263 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6918 (mp) REVERT: D 333 LYS cc_start: 0.6656 (tptt) cc_final: 0.5753 (mtmp) outliers start: 42 outliers final: 22 residues processed: 114 average time/residue: 0.4694 time to fit residues: 56.6077 Evaluate side-chains 115 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 56 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** D 359 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 = 0.4382 r_free = 0.4382 target = 0.208698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164552 restraints weight = 6410.398| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.43 r_work: 0.3822 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6200 Z= 0.146 Angle : 0.603 8.538 8412 Z= 0.300 Chirality : 0.049 0.610 932 Planarity : 0.004 0.042 1080 Dihedral : 5.972 45.328 957 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 6.28 % Allowed : 26.46 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.53 (0.31), residues: 755 helix: 0.26 (1.11), residues: 20 sheet: -1.72 (0.43), residues: 136 loop : -0.94 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 278 TYR 0.019 0.001 TYR D 308 PHE 0.013 0.002 PHE A 54 TRP 0.010 0.001 TRP D 163 HIS 0.007 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6175) covalent geometry : angle 0.57872 ( 8356) SS BOND : bond 0.00419 ( 19) SS BOND : angle 1.32043 ( 38) hydrogen bonds : bond 0.02960 ( 120) hydrogen bonds : angle 6.01391 ( 285) link_BETA1-4 : bond 0.00268 ( 2) link_BETA1-4 : angle 1.75454 ( 6) link_NAG-ASN : bond 0.01338 ( 4) link_NAG-ASN : angle 3.81989 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7044 (tmtt) cc_final: 0.6700 (tmtt) REVERT: A 23 HIS cc_start: 0.3560 (OUTLIER) cc_final: 0.3070 (m170) REVERT: A 35 GLU cc_start: 0.7659 (tt0) cc_final: 0.6968 (tm-30) REVERT: A 125 ARG cc_start: 0.7389 (ttt180) cc_final: 0.6299 (tpt-90) REVERT: A 295 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: A 331 ASN cc_start: 0.7103 (m-40) cc_final: 0.6702 (m110) REVERT: A 367 GLU cc_start: 0.7372 (mp0) cc_final: 0.6985 (mp0) REVERT: A 370 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 388 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: A 400 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 446 CYS cc_start: 0.5855 (OUTLIER) cc_final: 0.5586 (t) REVERT: A 455 LYS cc_start: 0.7255 (ttpp) cc_final: 0.6537 (ttpp) REVERT: A 524 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: A 561 TYR cc_start: 0.6851 (m-80) cc_final: 0.5931 (m-80) REVERT: A 594 HIS cc_start: 0.8128 (m170) cc_final: 0.7570 (m170) REVERT: D 263 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6925 (mp) REVERT: D 333 LYS cc_start: 0.6607 (tptt) cc_final: 0.5737 (mtmp) REVERT: D 364 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6946 (pt0) outliers start: 42 outliers final: 22 residues processed: 111 average time/residue: 0.5103 time to fit residues: 59.9407 Evaluate side-chains 110 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.0020 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.207128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156119 restraints weight = 6421.358| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.46 r_work: 0.3747 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6200 Z= 0.186 Angle : 0.632 8.474 8412 Z= 0.315 Chirality : 0.050 0.615 932 Planarity : 0.004 0.040 1080 Dihedral : 6.145 47.744 957 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 6.28 % Allowed : 26.91 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.61 (0.31), residues: 755 helix: 0.10 (1.08), residues: 20 sheet: -1.87 (0.42), residues: 143 loop : -0.94 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 278 TYR 0.024 0.002 TYR D 308 PHE 0.018 0.002 PHE A 31 TRP 0.012 0.002 TRP D 163 HIS 0.007 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6175) covalent geometry : angle 0.60788 ( 8356) SS BOND : bond 0.00485 ( 19) SS BOND : angle 1.41224 ( 38) hydrogen bonds : bond 0.03092 ( 120) hydrogen bonds : angle 6.06010 ( 285) link_BETA1-4 : bond 0.00243 ( 2) link_BETA1-4 : angle 1.88186 ( 6) link_NAG-ASN : bond 0.01224 ( 4) link_NAG-ASN : angle 3.83666 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7007 (tmtt) cc_final: 0.6639 (tmtt) REVERT: A 23 HIS cc_start: 0.3622 (OUTLIER) cc_final: 0.3091 (m170) REVERT: A 35 GLU cc_start: 0.7690 (tt0) cc_final: 0.6935 (tm-30) REVERT: A 60 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: A 125 ARG cc_start: 0.7424 (ttt180) cc_final: 0.6316 (tpt-90) REVERT: A 188 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.5542 (tppt) REVERT: A 295 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: A 367 GLU cc_start: 0.7384 (mp0) cc_final: 0.7007 (mp0) REVERT: A 370 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7309 (mp) REVERT: A 400 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: A 446 CYS cc_start: 0.5867 (OUTLIER) cc_final: 0.5584 (t) REVERT: A 455 LYS cc_start: 0.7235 (ttpp) cc_final: 0.6487 (ttpp) REVERT: A 489 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 524 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6595 (mt-10) REVERT: A 544 ASN cc_start: 0.6613 (m110) cc_final: 0.6169 (m-40) REVERT: A 561 TYR cc_start: 0.6813 (m-80) cc_final: 0.5862 (m-80) REVERT: A 594 HIS cc_start: 0.8071 (m170) cc_final: 0.7504 (m170) REVERT: D 333 LYS cc_start: 0.6587 (tptt) cc_final: 0.5684 (mtmp) REVERT: D 364 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6973 (pt0) outliers start: 42 outliers final: 23 residues processed: 116 average time/residue: 0.5057 time to fit residues: 62.0470 Evaluate side-chains 112 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 63 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** D 359 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 = 0.4389 r_free = 0.4389 target = 0.209745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158532 restraints weight = 6474.437| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.52 r_work: 0.3778 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6200 Z= 0.132 Angle : 0.602 8.637 8412 Z= 0.299 Chirality : 0.049 0.575 932 Planarity : 0.004 0.043 1080 Dihedral : 5.754 44.258 955 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.78 % Allowed : 28.40 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.49 (0.31), residues: 755 helix: 0.14 (1.10), residues: 20 sheet: -1.67 (0.43), residues: 136 loop : -0.91 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 278 TYR 0.017 0.001 TYR D 308 PHE 0.022 0.002 PHE A 31 TRP 0.010 0.001 TRP D 163 HIS 0.007 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6175) covalent geometry : angle 0.58076 ( 8356) SS BOND : bond 0.00328 ( 19) SS BOND : angle 1.08953 ( 38) hydrogen bonds : bond 0.02814 ( 120) hydrogen bonds : angle 5.83564 ( 285) link_BETA1-4 : bond 0.00233 ( 2) link_BETA1-4 : angle 1.84066 ( 6) link_NAG-ASN : bond 0.01476 ( 4) link_NAG-ASN : angle 3.75076 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7045 (tmtt) cc_final: 0.6690 (tmtt) REVERT: A 23 HIS cc_start: 0.3643 (OUTLIER) cc_final: 0.3116 (m170) REVERT: A 35 GLU cc_start: 0.7674 (tt0) cc_final: 0.7001 (tm-30) REVERT: A 60 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: A 125 ARG cc_start: 0.7415 (ttt180) cc_final: 0.6268 (tpt-90) REVERT: A 188 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5562 (tppt) REVERT: A 295 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: A 331 ASN cc_start: 0.7070 (m-40) cc_final: 0.6223 (m-40) REVERT: A 367 GLU cc_start: 0.7354 (mp0) cc_final: 0.6951 (mp0) REVERT: A 370 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7192 (mp) REVERT: A 400 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 446 CYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5671 (t) REVERT: A 455 LYS cc_start: 0.7202 (ttpp) cc_final: 0.6462 (ttpp) REVERT: A 489 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7088 (mt-10) REVERT: A 544 ASN cc_start: 0.6465 (m110) cc_final: 0.5991 (m-40) REVERT: A 561 TYR cc_start: 0.6847 (m-80) cc_final: 0.5882 (m-80) REVERT: A 594 HIS cc_start: 0.8119 (m170) cc_final: 0.7569 (m170) REVERT: D 333 LYS cc_start: 0.6603 (tptt) cc_final: 0.6334 (mmmm) outliers start: 32 outliers final: 21 residues processed: 106 average time/residue: 0.5065 time to fit residues: 56.8532 Evaluate side-chains 108 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 0.0010 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 69 optimal weight: 0.2980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.208928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165515 restraints weight = 6392.613| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.37 r_work: 0.3844 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6200 Z= 0.139 Angle : 0.606 8.547 8412 Z= 0.301 Chirality : 0.049 0.548 932 Planarity : 0.004 0.042 1080 Dihedral : 5.781 44.310 955 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.78 % Allowed : 28.85 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.45 (0.31), residues: 755 helix: 0.12 (1.09), residues: 20 sheet: -1.54 (0.46), residues: 126 loop : -0.92 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 278 TYR 0.018 0.001 TYR D 308 PHE 0.026 0.002 PHE A 31 TRP 0.011 0.001 TRP D 163 HIS 0.006 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6175) covalent geometry : angle 0.58489 ( 8356) SS BOND : bond 0.00360 ( 19) SS BOND : angle 1.15166 ( 38) hydrogen bonds : bond 0.02812 ( 120) hydrogen bonds : angle 5.77286 ( 285) link_BETA1-4 : bond 0.00327 ( 2) link_BETA1-4 : angle 1.82168 ( 6) link_NAG-ASN : bond 0.01784 ( 4) link_NAG-ASN : angle 3.64780 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6948 (tmtt) cc_final: 0.6584 (tmtt) REVERT: A 23 HIS cc_start: 0.3652 (OUTLIER) cc_final: 0.3112 (m170) REVERT: A 35 GLU cc_start: 0.7589 (tt0) cc_final: 0.6867 (tm-30) REVERT: A 125 ARG cc_start: 0.7395 (ttt180) cc_final: 0.6250 (tpt90) REVERT: A 188 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5467 (tppt) REVERT: A 295 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: A 331 ASN cc_start: 0.6970 (m-40) cc_final: 0.6190 (m-40) REVERT: A 367 GLU cc_start: 0.7285 (mp0) cc_final: 0.6876 (mp0) REVERT: A 370 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7128 (mp) REVERT: A 400 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: A 446 CYS cc_start: 0.5813 (OUTLIER) cc_final: 0.5551 (t) REVERT: A 455 LYS cc_start: 0.7164 (ttpp) cc_final: 0.6473 (ttpp) REVERT: A 489 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 544 ASN cc_start: 0.6393 (m110) cc_final: 0.5920 (m-40) REVERT: A 561 TYR cc_start: 0.6878 (m-80) cc_final: 0.5875 (m-80) REVERT: A 594 HIS cc_start: 0.8132 (m170) cc_final: 0.7564 (m170) REVERT: D 162 GLU cc_start: 0.8152 (tt0) cc_final: 0.7856 (pt0) REVERT: D 263 LEU cc_start: 0.7572 (mt) cc_final: 0.7216 (mp) REVERT: D 333 LYS cc_start: 0.6488 (tptt) cc_final: 0.6209 (mmmm) outliers start: 32 outliers final: 21 residues processed: 103 average time/residue: 0.5133 time to fit residues: 55.9426 Evaluate side-chains 108 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.209147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157527 restraints weight = 6460.007| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.52 r_work: 0.3763 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6200 Z= 0.155 Angle : 0.625 8.385 8412 Z= 0.312 Chirality : 0.049 0.455 932 Planarity : 0.004 0.042 1080 Dihedral : 5.869 44.721 955 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.08 % Allowed : 28.85 % Favored : 66.07 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.51 (0.31), residues: 755 helix: 0.02 (1.07), residues: 20 sheet: -1.72 (0.44), residues: 133 loop : -0.91 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 278 TYR 0.020 0.001 TYR D 308 PHE 0.026 0.002 PHE A 31 TRP 0.012 0.001 TRP D 163 HIS 0.006 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6175) covalent geometry : angle 0.60710 ( 8356) SS BOND : bond 0.00385 ( 19) SS BOND : angle 1.20536 ( 38) hydrogen bonds : bond 0.03082 ( 120) hydrogen bonds : angle 5.72186 ( 285) link_BETA1-4 : bond 0.00307 ( 2) link_BETA1-4 : angle 1.73295 ( 6) link_NAG-ASN : bond 0.01702 ( 4) link_NAG-ASN : angle 3.27124 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.05 seconds wall clock time: 51 minutes 56.47 seconds (3116.47 seconds total)