Starting phenix.real_space_refine on Thu Jun 5 11:38:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipb_60768/06_2025/9ipb_60768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipb_60768/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ipb_60768/06_2025/9ipb_60768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipb_60768/06_2025/9ipb_60768.map" model { file = "/net/cci-nas-00/data/ceres_data/9ipb_60768/06_2025/9ipb_60768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipb_60768/06_2025/9ipb_60768.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.18, per 1000 atoms: 0.86 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.94 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: 2.09 Time building geometry restraints manager: 1.85 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.560 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.200 ------------------------------------------------------------------------------- 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 : 14.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (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 TRP 0.017 0.002 TRP A 453 HIS 0.002 0.000 HIS A 566 PHE 0.015 0.001 PHE D 145 TYR 0.025 0.002 TYR D 308 ARG 0.008 0.001 ARG A 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 4) link_NAG-ASN : angle 3.16040 ( 12) link_BETA1-4 : bond 0.00467 ( 2) link_BETA1-4 : angle 1.62752 ( 6) hydrogen bonds : bond 0.25338 ( 120) hydrogen bonds : angle 9.93395 ( 285) SS BOND : bond 0.00419 ( 19) SS BOND : angle 1.30593 ( 38) covalent geometry : bond 0.00800 ( 6175) covalent geometry : angle 1.06196 ( 8356) *********************** 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 : 0.699 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: 1.0723 time to fit residues: 123.5417 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 : 0.707 ------------------------------------------------------------------------------- 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 64 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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 = 0.4377 r_free = 0.4377 target = 0.210226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159688 restraints weight = 6222.342| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.44 r_work: 0.3799 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6200 Z= 0.174 Angle : 0.633 9.703 8412 Z= 0.321 Chirality : 0.049 0.530 932 Planarity : 0.004 0.036 1080 Dihedral : 7.343 108.723 964 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.28 % Allowed : 22.87 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.31), residues: 755 helix: 0.20 (1.01), residues: 20 sheet: -1.91 (0.42), residues: 138 loop : -1.02 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 163 HIS 0.009 0.001 HIS A 23 PHE 0.019 0.002 PHE D 220 TYR 0.022 0.002 TYR D 308 ARG 0.004 0.001 ARG A 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 4) link_NAG-ASN : angle 3.55749 ( 12) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 1.66294 ( 6) hydrogen bonds : bond 0.04043 ( 120) hydrogen bonds : angle 7.08348 ( 285) SS BOND : bond 0.00466 ( 19) SS BOND : angle 1.19059 ( 38) covalent geometry : bond 0.00396 ( 6175) covalent geometry : angle 0.61365 ( 8356) *********************** 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 132 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6895 (tmtt) cc_final: 0.6485 (tttt) REVERT: A 23 HIS cc_start: 0.3611 (OUTLIER) cc_final: 0.3298 (m170) REVERT: A 35 GLU cc_start: 0.7715 (tt0) cc_final: 0.6894 (tm-30) REVERT: A 60 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: A 125 ARG cc_start: 0.7396 (ttt180) cc_final: 0.6316 (tpt-90) REVERT: A 388 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: A 455 LYS cc_start: 0.7222 (ttpp) cc_final: 0.6552 (ttpp) REVERT: A 483 HIS cc_start: 0.6159 (OUTLIER) cc_final: 0.5466 (m170) REVERT: A 524 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.5849 (mm-30) REVERT: A 535 HIS cc_start: 0.7741 (t-90) cc_final: 0.7411 (t-90) REVERT: A 561 TYR cc_start: 0.6779 (m-80) cc_final: 0.6159 (m-80) REVERT: D 263 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6883 (tp) REVERT: D 333 LYS cc_start: 0.6682 (tptt) cc_final: 0.5744 (mtmm) outliers start: 42 outliers final: 16 residues processed: 120 average time/residue: 0.9955 time to fit residues: 126.5358 Evaluate side-chains 104 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain A residue 350 VAL 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 61 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 D 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.210478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159817 restraints weight = 6292.776| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.46 r_work: 0.3818 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6200 Z= 0.150 Angle : 0.597 8.256 8412 Z= 0.303 Chirality : 0.049 0.564 932 Planarity : 0.004 0.036 1080 Dihedral : 5.984 45.046 959 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 6.28 % Allowed : 24.66 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.31), residues: 755 helix: 0.48 (1.09), residues: 20 sheet: -1.67 (0.44), residues: 132 loop : -0.99 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.008 0.001 HIS A 23 PHE 0.016 0.002 PHE A 31 TYR 0.019 0.001 TYR D 308 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 4) link_NAG-ASN : angle 3.75200 ( 12) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 1.56416 ( 6) hydrogen bonds : bond 0.03580 ( 120) hydrogen bonds : angle 6.58357 ( 285) SS BOND : bond 0.00419 ( 19) SS BOND : angle 1.07292 ( 38) covalent geometry : bond 0.00342 ( 6175) covalent geometry : angle 0.57538 ( 8356) *********************** 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 126 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7002 (tmtt) cc_final: 0.6640 (tmtt) REVERT: A 23 HIS cc_start: 0.3636 (OUTLIER) cc_final: 0.3264 (m170) REVERT: A 35 GLU cc_start: 0.7739 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 60 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: A 125 ARG cc_start: 0.7445 (ttt180) cc_final: 0.6269 (tpt-90) REVERT: A 294 MET cc_start: 0.6114 (tpt) cc_final: 0.5830 (tpt) REVERT: A 388 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: A 446 CYS cc_start: 0.5788 (OUTLIER) cc_final: 0.5541 (t) REVERT: A 455 LYS cc_start: 0.7260 (ttpp) cc_final: 0.6557 (ttpp) REVERT: A 524 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: A 535 HIS cc_start: 0.7770 (t-90) cc_final: 0.7513 (t-90) REVERT: A 537 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6819 (mm-30) REVERT: A 561 TYR cc_start: 0.6770 (m-80) cc_final: 0.6070 (m-80) REVERT: D 119 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: D 263 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6770 (mp) REVERT: D 333 LYS cc_start: 0.6639 (tptt) cc_final: 0.5702 (mtmp) outliers start: 42 outliers final: 15 residues processed: 113 average time/residue: 1.0477 time to fit residues: 125.1923 Evaluate side-chains 106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 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 524 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 6 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.210228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159645 restraints weight = 6420.033| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.50 r_work: 0.3797 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6200 Z= 0.143 Angle : 0.590 8.183 8412 Z= 0.294 Chirality : 0.049 0.580 932 Planarity : 0.004 0.038 1080 Dihedral : 5.930 44.709 959 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.98 % Allowed : 24.81 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.31), residues: 755 helix: 0.40 (1.09), residues: 20 sheet: -1.71 (0.44), residues: 132 loop : -0.95 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.008 0.001 HIS A 23 PHE 0.029 0.002 PHE A 31 TYR 0.019 0.001 TYR D 308 ARG 0.006 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.01027 ( 4) link_NAG-ASN : angle 3.79425 ( 12) link_BETA1-4 : bond 0.00218 ( 2) link_BETA1-4 : angle 1.76921 ( 6) hydrogen bonds : bond 0.03225 ( 120) hydrogen bonds : angle 6.29865 ( 285) SS BOND : bond 0.00388 ( 19) SS BOND : angle 1.06995 ( 38) covalent geometry : bond 0.00331 ( 6175) covalent geometry : angle 0.56797 ( 8356) *********************** 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 129 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7002 (tmtt) cc_final: 0.6628 (tmtt) REVERT: A 23 HIS cc_start: 0.3588 (OUTLIER) cc_final: 0.3181 (m170) REVERT: A 31 PHE cc_start: 0.7455 (m-80) cc_final: 0.7185 (m-80) REVERT: A 35 GLU cc_start: 0.7709 (tt0) cc_final: 0.6948 (tm-30) REVERT: A 60 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: A 125 ARG cc_start: 0.7417 (ttt180) cc_final: 0.6253 (tpt-90) REVERT: A 295 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: A 367 GLU cc_start: 0.7306 (mp0) cc_final: 0.7083 (mp0) REVERT: A 388 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: A 446 CYS cc_start: 0.5783 (OUTLIER) cc_final: 0.5534 (t) REVERT: A 455 LYS cc_start: 0.7219 (ttpp) cc_final: 0.6495 (ttpp) REVERT: A 535 HIS cc_start: 0.7725 (t-90) cc_final: 0.7514 (t-90) REVERT: A 537 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6725 (mm-30) REVERT: A 561 TYR cc_start: 0.6772 (m-80) cc_final: 0.6023 (m-80) REVERT: D 119 GLN cc_start: 0.7819 (tt0) cc_final: 0.7567 (tm-30) REVERT: D 263 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6847 (mp) REVERT: D 278 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6354 (mmm160) REVERT: D 333 LYS cc_start: 0.6584 (tptt) cc_final: 0.5670 (mtmp) outliers start: 40 outliers final: 17 residues processed: 118 average time/residue: 1.1203 time to fit residues: 139.2143 Evaluate side-chains 107 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 350 VAL 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 495 GLU 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 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 58 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 54 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.212239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162028 restraints weight = 6345.476| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.46 r_work: 0.3815 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6200 Z= 0.117 Angle : 0.562 7.968 8412 Z= 0.280 Chirality : 0.048 0.584 932 Planarity : 0.004 0.040 1080 Dihedral : 5.736 42.323 957 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.83 % Allowed : 25.86 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.31), residues: 755 helix: 0.42 (1.11), residues: 20 sheet: -1.65 (0.44), residues: 132 loop : -0.91 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.007 0.001 HIS A 23 PHE 0.030 0.002 PHE A 31 TYR 0.014 0.001 TYR D 308 ARG 0.002 0.000 ARG A 84 Details of bonding type rmsd link_NAG-ASN : bond 0.01117 ( 4) link_NAG-ASN : angle 3.76092 ( 12) link_BETA1-4 : bond 0.00321 ( 2) link_BETA1-4 : angle 1.77329 ( 6) hydrogen bonds : bond 0.02884 ( 120) hydrogen bonds : angle 5.96008 ( 285) SS BOND : bond 0.00325 ( 19) SS BOND : angle 0.87530 ( 38) covalent geometry : bond 0.00266 ( 6175) covalent geometry : angle 0.54013 ( 8356) *********************** 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 124 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7042 (tmtt) cc_final: 0.6621 (tttt) REVERT: A 23 HIS cc_start: 0.3555 (OUTLIER) cc_final: 0.3150 (m170) REVERT: A 35 GLU cc_start: 0.7703 (tt0) cc_final: 0.6991 (tm-30) REVERT: A 125 ARG cc_start: 0.7420 (ttt180) cc_final: 0.6272 (tpt-90) REVERT: A 295 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: A 309 CYS cc_start: 0.5254 (OUTLIER) cc_final: 0.4967 (t) REVERT: A 331 ASN cc_start: 0.7120 (m-40) cc_final: 0.6704 (m110) REVERT: A 367 GLU cc_start: 0.7406 (mp0) cc_final: 0.7156 (mp0) REVERT: A 388 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: A 400 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: A 446 CYS cc_start: 0.5784 (OUTLIER) cc_final: 0.5536 (t) REVERT: A 455 LYS cc_start: 0.7178 (ttpp) cc_final: 0.6512 (ttpp) REVERT: A 561 TYR cc_start: 0.6811 (m-80) cc_final: 0.6034 (m-80) REVERT: D 263 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6890 (mp) REVERT: D 333 LYS cc_start: 0.6581 (tptt) cc_final: 0.5690 (mtmp) outliers start: 39 outliers final: 17 residues processed: 111 average time/residue: 1.2375 time to fit residues: 144.8551 Evaluate side-chains 101 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS 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 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 497 ARG Chi-restraints excluded: chain A residue 546 THR 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 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 0.0270 chunk 74 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 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 = 0.4401 r_free = 0.4401 target = 0.211709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159272 restraints weight = 6309.370| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.56 r_work: 0.3804 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1991 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 : 0.591 8.256 8412 Z= 0.292 Chirality : 0.049 0.562 932 Planarity : 0.004 0.043 1080 Dihedral : 5.794 42.983 957 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.68 % Allowed : 27.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.31), residues: 755 helix: 0.32 (1.11), residues: 20 sheet: -1.58 (0.44), residues: 132 loop : -0.92 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.007 0.001 HIS A 23 PHE 0.027 0.002 PHE A 31 TYR 0.020 0.001 TYR D 308 ARG 0.002 0.000 ARG A 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00943 ( 4) link_NAG-ASN : angle 3.66748 ( 12) link_BETA1-4 : bond 0.00310 ( 2) link_BETA1-4 : angle 1.68820 ( 6) hydrogen bonds : bond 0.02997 ( 120) hydrogen bonds : angle 5.89820 ( 285) SS BOND : bond 0.00396 ( 19) SS BOND : angle 1.16411 ( 38) covalent geometry : bond 0.00323 ( 6175) covalent geometry : angle 0.56893 ( 8356) *********************** 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 123 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7019 (tmtt) cc_final: 0.6597 (tttt) REVERT: A 23 HIS cc_start: 0.3509 (OUTLIER) cc_final: 0.3057 (m170) REVERT: A 35 GLU cc_start: 0.7705 (tt0) cc_final: 0.6945 (tm-30) REVERT: A 60 GLU cc_start: 0.7978 (tp30) cc_final: 0.7589 (tp30) REVERT: A 125 ARG cc_start: 0.7395 (ttt180) cc_final: 0.6246 (tpt-90) REVERT: A 293 GLU cc_start: 0.7148 (mp0) cc_final: 0.6875 (mp0) REVERT: A 295 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: A 300 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6093 (ttm110) REVERT: A 309 CYS cc_start: 0.5342 (OUTLIER) cc_final: 0.5126 (t) REVERT: A 367 GLU cc_start: 0.7406 (mp0) cc_final: 0.7021 (mp0) REVERT: A 370 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7278 (mp) REVERT: A 388 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: A 400 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: A 446 CYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5500 (t) REVERT: A 455 LYS cc_start: 0.7201 (ttpp) cc_final: 0.6536 (ttpp) REVERT: A 524 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6481 (mt-10) REVERT: A 561 TYR cc_start: 0.6810 (m-80) cc_final: 0.5943 (m-80) REVERT: D 119 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: D 263 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6839 (mp) REVERT: D 333 LYS cc_start: 0.6542 (tptt) cc_final: 0.6162 (mmmm) outliers start: 38 outliers final: 20 residues processed: 112 average time/residue: 1.2291 time to fit residues: 145.3904 Evaluate side-chains 112 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 487 SER 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 562 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain D residue 119 GLN 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 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 50 optimal weight: 0.0070 chunk 43 optimal weight: 0.0060 chunk 67 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 469 ASN ** A 516 ASN ** 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 = 0.4415 r_free = 0.4415 target = 0.213213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.161220 restraints weight = 6379.279| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.57 r_work: 0.3837 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6200 Z= 0.116 Angle : 0.570 7.675 8412 Z= 0.282 Chirality : 0.048 0.563 932 Planarity : 0.004 0.040 1080 Dihedral : 5.649 41.997 957 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.68 % Allowed : 27.35 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.31), residues: 755 helix: 0.28 (1.11), residues: 20 sheet: -1.59 (0.43), residues: 136 loop : -0.92 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.007 0.001 HIS A 23 PHE 0.028 0.002 PHE A 31 TYR 0.015 0.001 TYR D 308 ARG 0.002 0.000 ARG D 278 Details of bonding type rmsd link_NAG-ASN : bond 0.01140 ( 4) link_NAG-ASN : angle 3.62304 ( 12) link_BETA1-4 : bond 0.00323 ( 2) link_BETA1-4 : angle 1.83820 ( 6) hydrogen bonds : bond 0.02930 ( 120) hydrogen bonds : angle 5.75430 ( 285) SS BOND : bond 0.00286 ( 19) SS BOND : angle 0.95725 ( 38) covalent geometry : bond 0.00263 ( 6175) covalent geometry : angle 0.54940 ( 8356) *********************** 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 124 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.720 Fit side-chains REVERT: A 5 LYS cc_start: 0.6990 (tmtt) cc_final: 0.6576 (tttt) REVERT: A 23 HIS cc_start: 0.3504 (OUTLIER) cc_final: 0.3044 (m170) REVERT: A 35 GLU cc_start: 0.7701 (tt0) cc_final: 0.6934 (tm-30) REVERT: A 60 GLU cc_start: 0.7942 (tp30) cc_final: 0.7497 (tp30) REVERT: A 125 ARG cc_start: 0.7312 (ttt180) cc_final: 0.6118 (tpt-90) REVERT: A 293 GLU cc_start: 0.7130 (mp0) cc_final: 0.6876 (mp0) REVERT: A 295 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: A 300 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6118 (ttm110) REVERT: A 309 CYS cc_start: 0.5233 (OUTLIER) cc_final: 0.4996 (t) REVERT: A 331 ASN cc_start: 0.7047 (m-40) cc_final: 0.6502 (t0) REVERT: A 367 GLU cc_start: 0.7331 (mp0) cc_final: 0.6934 (mp0) REVERT: A 370 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7111 (mp) REVERT: A 388 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: A 400 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: A 446 CYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5541 (t) REVERT: A 455 LYS cc_start: 0.7171 (ttpp) cc_final: 0.6491 (ttpp) REVERT: A 489 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6884 (mt-10) REVERT: A 524 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6590 (mt-10) REVERT: A 561 TYR cc_start: 0.6804 (m-80) cc_final: 0.5900 (m-80) REVERT: D 119 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: D 263 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6839 (mp) REVERT: D 333 LYS cc_start: 0.6510 (tptt) cc_final: 0.6235 (mmmm) outliers start: 38 outliers final: 19 residues processed: 113 average time/residue: 1.0341 time to fit residues: 123.3160 Evaluate side-chains 112 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 400 GLU Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 487 SER 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 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 119 GLN Chi-restraints excluded: chain D residue 127 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 72 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 211 GLN A 384 GLN ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.211706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159408 restraints weight = 6343.264| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.55 r_work: 0.3818 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.003 0.036 6200 Z= 0.137 Angle : 0.593 8.313 8412 Z= 0.294 Chirality : 0.049 0.556 932 Planarity : 0.004 0.041 1080 Dihedral : 5.723 41.833 957 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.28 % Allowed : 27.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.31), residues: 755 helix: 0.32 (1.11), residues: 20 sheet: -1.56 (0.43), residues: 136 loop : -0.93 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 163 HIS 0.007 0.001 HIS A 23 PHE 0.023 0.002 PHE A 31 TYR 0.019 0.001 TYR D 308 ARG 0.003 0.000 ARG D 278 Details of bonding type rmsd link_NAG-ASN : bond 0.01233 ( 4) link_NAG-ASN : angle 3.73064 ( 12) link_BETA1-4 : bond 0.00272 ( 2) link_BETA1-4 : angle 1.75971 ( 6) hydrogen bonds : bond 0.02918 ( 120) hydrogen bonds : angle 5.73975 ( 285) SS BOND : bond 0.00341 ( 19) SS BOND : angle 1.04428 ( 38) covalent geometry : bond 0.00316 ( 6175) covalent geometry : angle 0.57131 ( 8356) *********************** 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 127 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7029 (tmtt) cc_final: 0.6617 (tttt) REVERT: A 23 HIS cc_start: 0.3651 (OUTLIER) cc_final: 0.3143 (m170) REVERT: A 35 GLU cc_start: 0.7724 (tt0) cc_final: 0.6963 (tm-30) REVERT: A 125 ARG cc_start: 0.7382 (ttt180) cc_final: 0.6219 (ttt-90) REVERT: A 134 ASN cc_start: 0.5879 (OUTLIER) cc_final: 0.5632 (t0) REVERT: A 295 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: A 300 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6172 (ttm110) REVERT: A 331 ASN cc_start: 0.7056 (m-40) cc_final: 0.6551 (t0) REVERT: A 367 GLU cc_start: 0.7316 (mp0) cc_final: 0.6938 (mp0) REVERT: A 370 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7144 (mp) REVERT: A 388 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: A 400 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: A 446 CYS cc_start: 0.5802 (OUTLIER) cc_final: 0.5546 (t) REVERT: A 455 LYS cc_start: 0.7180 (ttpp) cc_final: 0.6501 (ttpp) REVERT: A 524 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: A 544 ASN cc_start: 0.6428 (m110) cc_final: 0.5992 (m-40) REVERT: A 561 TYR cc_start: 0.6819 (m-80) cc_final: 0.5845 (m-80) REVERT: A 594 HIS cc_start: 0.8026 (m170) cc_final: 0.7493 (m170) REVERT: D 162 GLU cc_start: 0.8173 (tt0) cc_final: 0.7959 (pt0) REVERT: D 263 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6884 (mp) REVERT: D 333 LYS cc_start: 0.6518 (tptt) cc_final: 0.6245 (mmmm) outliers start: 42 outliers final: 20 residues processed: 114 average time/residue: 1.0271 time to fit residues: 123.9000 Evaluate side-chains 111 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 138 ILE 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 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 562 ILE Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain D residue 127 VAL 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 344 VAL Chi-restraints excluded: chain D residue 352 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 2 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 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.208412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.156057 restraints weight = 6413.166| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.53 r_work: 0.3753 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6200 Z= 0.195 Angle : 0.650 8.260 8412 Z= 0.324 Chirality : 0.051 0.605 932 Planarity : 0.004 0.037 1080 Dihedral : 5.992 45.444 957 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.83 % Allowed : 27.50 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.31), residues: 755 helix: 0.13 (1.08), residues: 20 sheet: -1.70 (0.44), residues: 133 loop : -0.95 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 163 HIS 0.007 0.001 HIS A 23 PHE 0.024 0.002 PHE A 31 TYR 0.027 0.002 TYR D 308 ARG 0.002 0.000 ARG D 278 Details of bonding type rmsd link_NAG-ASN : bond 0.01539 ( 4) link_NAG-ASN : angle 3.78535 ( 12) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 1.83586 ( 6) hydrogen bonds : bond 0.03226 ( 120) hydrogen bonds : angle 5.86792 ( 285) SS BOND : bond 0.00534 ( 19) SS BOND : angle 1.43870 ( 38) covalent geometry : bond 0.00456 ( 6175) covalent geometry : angle 0.62639 ( 8356) *********************** 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 121 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7146 (tmtt) cc_final: 0.6741 (tttt) REVERT: A 23 HIS cc_start: 0.3700 (OUTLIER) cc_final: 0.3097 (m170) REVERT: A 35 GLU cc_start: 0.7764 (tt0) cc_final: 0.7009 (tm-30) REVERT: A 125 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6383 (tpt90) REVERT: A 134 ASN cc_start: 0.6037 (OUTLIER) cc_final: 0.5826 (t0) REVERT: A 188 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.5583 (tppt) REVERT: A 295 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: A 367 GLU cc_start: 0.7394 (mp0) cc_final: 0.7027 (mp0) REVERT: A 370 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7271 (mp) REVERT: A 388 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: A 400 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: A 446 CYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5659 (t) REVERT: A 455 LYS cc_start: 0.7246 (ttpp) cc_final: 0.6513 (ttpp) REVERT: A 489 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 524 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: A 544 ASN cc_start: 0.6488 (m110) cc_final: 0.6039 (m-40) REVERT: A 561 TYR cc_start: 0.6835 (m-80) cc_final: 0.5869 (m-80) REVERT: A 594 HIS cc_start: 0.8033 (m170) cc_final: 0.7511 (m170) REVERT: D 162 GLU cc_start: 0.8214 (tt0) cc_final: 0.7979 (pt0) REVERT: D 333 LYS cc_start: 0.6614 (tptt) cc_final: 0.5752 (mtmp) outliers start: 39 outliers final: 24 residues processed: 106 average time/residue: 1.0110 time to fit residues: 113.4604 Evaluate side-chains 111 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 138 ILE 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 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 320 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 535 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.207314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154884 restraints weight = 6461.130| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.52 r_work: 0.3741 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6200 Z= 0.207 Angle : 0.663 8.488 8412 Z= 0.332 Chirality : 0.051 0.582 932 Planarity : 0.004 0.040 1080 Dihedral : 6.046 48.000 955 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.31), residues: 755 helix: 0.03 (1.07), residues: 20 sheet: -1.63 (0.45), residues: 131 loop : -1.01 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 163 HIS 0.006 0.001 HIS A 23 PHE 0.027 0.003 PHE A 31 TYR 0.029 0.002 TYR D 308 ARG 0.002 0.000 ARG D 278 Details of bonding type rmsd link_NAG-ASN : bond 0.01736 ( 4) link_NAG-ASN : angle 3.72813 ( 12) link_BETA1-4 : bond 0.00204 ( 2) link_BETA1-4 : angle 1.95688 ( 6) hydrogen bonds : bond 0.03301 ( 120) hydrogen bonds : angle 5.95897 ( 285) SS BOND : bond 0.00534 ( 19) SS BOND : angle 1.58650 ( 38) covalent geometry : bond 0.00484 ( 6175) covalent geometry : angle 0.63865 ( 8356) ********************** 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 114 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7076 (tmtt) cc_final: 0.6696 (tmtt) REVERT: A 23 HIS cc_start: 0.3705 (OUTLIER) cc_final: 0.3062 (m170) REVERT: A 35 GLU cc_start: 0.7749 (tt0) cc_final: 0.6920 (tm-30) REVERT: A 125 ARG cc_start: 0.7400 (ttt180) cc_final: 0.6283 (tpt90) REVERT: A 295 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: A 367 GLU cc_start: 0.7374 (mp0) cc_final: 0.7024 (mp0) REVERT: A 370 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7318 (mp) REVERT: A 400 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 446 CYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5622 (t) REVERT: A 455 LYS cc_start: 0.7261 (ttpp) cc_final: 0.6487 (ttpp) REVERT: A 489 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 524 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: A 535 HIS cc_start: 0.7664 (t70) cc_final: 0.7365 (t70) REVERT: A 544 ASN cc_start: 0.6467 (m110) cc_final: 0.5988 (m-40) REVERT: A 561 TYR cc_start: 0.6882 (m-80) cc_final: 0.5865 (m-80) REVERT: A 594 HIS cc_start: 0.7905 (m170) cc_final: 0.7383 (m170) REVERT: D 162 GLU cc_start: 0.8238 (tt0) cc_final: 0.8016 (pt0) REVERT: D 263 LEU cc_start: 0.7553 (mt) cc_final: 0.7206 (mp) REVERT: D 333 LYS cc_start: 0.6564 (tptt) cc_final: 0.6290 (mmmm) outliers start: 32 outliers final: 23 residues processed: 102 average time/residue: 1.1939 time to fit residues: 128.9566 Evaluate side-chains 108 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 320 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.207523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.163057 restraints weight = 6448.110| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.39 r_work: 0.3788 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6200 Z= 0.173 Angle : 0.643 8.696 8412 Z= 0.322 Chirality : 0.049 0.450 932 Planarity : 0.004 0.040 1080 Dihedral : 6.008 47.306 955 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.93 % Allowed : 29.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.31), residues: 755 helix: -0.02 (1.06), residues: 20 sheet: -1.46 (0.46), residues: 124 loop : -0.99 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 163 HIS 0.006 0.001 HIS A 23 PHE 0.023 0.002 PHE A 31 TYR 0.024 0.002 TYR D 308 ARG 0.002 0.000 ARG D 278 Details of bonding type rmsd link_NAG-ASN : bond 0.01585 ( 4) link_NAG-ASN : angle 3.32086 ( 12) link_BETA1-4 : bond 0.00199 ( 2) link_BETA1-4 : angle 1.82090 ( 6) hydrogen bonds : bond 0.03114 ( 120) hydrogen bonds : angle 5.88094 ( 285) SS BOND : bond 0.00456 ( 19) SS BOND : angle 1.38372 ( 38) covalent geometry : bond 0.00402 ( 6175) covalent geometry : angle 0.62429 ( 8356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6178.57 seconds wall clock time: 107 minutes 44.29 seconds (6464.29 seconds total)