Starting phenix.real_space_refine on Tue Jan 13 13:39:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yj3_33870/01_2026/7yj3_33870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yj3_33870/01_2026/7yj3_33870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yj3_33870/01_2026/7yj3_33870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yj3_33870/01_2026/7yj3_33870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yj3_33870/01_2026/7yj3_33870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yj3_33870/01_2026/7yj3_33870.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4173 2.51 5 N 1074 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.73, per 1000 atoms: 0.27 Number of scatterers: 6518 At special positions: 0 Unit cell: (76.5, 91.8, 119.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1233 8.00 N 1074 7.00 C 4173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 NAG-ASN " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 53 " " NAG A 704 " - " ASN A 90 " " NAG A 705 " - " ASN A 103 " " NAG A 706 " - " ASN A 546 " " NAG A 707 " - " ASN A 322 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 244.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 54.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.575A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.511A pdb=" N GLY A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.654A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.700A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.511A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 157 through 174 removed outlier: 3.583A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 5.403A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.951A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.790A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.613A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.582A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.882A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.544A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.325A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.041A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.571A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.522A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.753A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.808A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.698A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.346A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.507A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.811A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.160A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.879A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 291 hydrogen bonds defined for protein. 816 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: 0.95 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1197 1.32 - 1.45: 1859 1.45 - 1.57: 3588 1.57 - 1.69: 0 1.69 - 1.82: 58 Bond restraints: 6702 Sorted by residual: bond pdb=" CE1 HIS A 34 " pdb=" NE2 HIS A 34 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.46e+01 bond pdb=" CA SER A 70 " pdb=" CB SER A 70 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.55e-02 4.16e+03 1.31e+01 bond pdb=" CE1 HIS A 505 " pdb=" NE2 HIS A 505 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" C PRO B 499 " pdb=" O PRO B 499 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.00e-02 1.00e+04 1.13e+01 bond pdb=" N ILE A 21 " pdb=" CA ILE A 21 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.41e-02 5.03e+03 9.90e+00 ... (remaining 6697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 8444 1.52 - 3.04: 499 3.04 - 4.56: 127 4.56 - 6.08: 30 6.08 - 7.61: 10 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 113.71 109.18 4.53 9.50e-01 1.11e+00 2.27e+01 angle pdb=" C PHE B 338 " pdb=" N ASP B 339 " pdb=" CA ASP B 339 " ideal model delta sigma weight residual 122.65 115.18 7.47 1.60e+00 3.91e-01 2.18e+01 angle pdb=" O ASN B 354 " pdb=" C ASN B 354 " pdb=" N ARG B 355 " ideal model delta sigma weight residual 122.89 117.70 5.19 1.22e+00 6.72e-01 1.81e+01 angle pdb=" CA GLY A 130 " pdb=" C GLY A 130 " pdb=" O GLY A 130 " ideal model delta sigma weight residual 120.94 117.73 3.21 7.80e-01 1.64e+00 1.69e+01 angle pdb=" N THR B 500 " pdb=" CA THR B 500 " pdb=" C THR B 500 " ideal model delta sigma weight residual 114.12 108.50 5.62 1.39e+00 5.18e-01 1.63e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3617 17.93 - 35.87: 330 35.87 - 53.80: 61 53.80 - 71.74: 28 71.74 - 89.67: 6 Dihedral angle restraints: 4042 sinusoidal: 1720 harmonic: 2322 Sorted by residual: dihedral pdb=" CD ARG B 457 " pdb=" NE ARG B 457 " pdb=" CZ ARG B 457 " pdb=" NH1 ARG B 457 " ideal model delta sinusoidal sigma weight residual 0.00 77.33 -77.33 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 169.52 -76.52 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CD ARG B 355 " pdb=" NE ARG B 355 " pdb=" CZ ARG B 355 " pdb=" NH1 ARG B 355 " ideal model delta sinusoidal sigma weight residual 0.00 -62.31 62.31 1 1.00e+01 1.00e-02 5.14e+01 ... (remaining 4039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 888 0.094 - 0.188: 75 0.188 - 0.282: 5 0.282 - 0.376: 0 0.376 - 0.470: 2 Chirality restraints: 970 Sorted by residual: chirality pdb=" C1 NAG A 705 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 705 " pdb=" O5 NAG A 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" C1 NAG A 707 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 707 " pdb=" O5 NAG A 707 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 967 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 707 " -0.290 2.00e-02 2.50e+03 2.49e-01 7.74e+02 pdb=" C7 NAG A 707 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 707 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A 707 " 0.437 2.00e-02 2.50e+03 pdb=" O7 NAG A 707 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 705 " 0.264 2.00e-02 2.50e+03 2.20e-01 6.03e+02 pdb=" C7 NAG A 705 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A 705 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 705 " -0.367 2.00e-02 2.50e+03 pdb=" O7 NAG A 705 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 457 " -1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG B 457 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 457 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 457 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 457 " -0.019 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 39 2.58 - 3.16: 5199 3.16 - 3.74: 9603 3.74 - 4.32: 13302 4.32 - 4.90: 22548 Nonbonded interactions: 50691 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 1.999 2.230 nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.169 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN A 90 " pdb=" N2 NAG A 704 " model vdw 2.281 3.120 nonbonded pdb=" O GLU A 224 " pdb=" ND1 HIS A 228 " model vdw 2.313 3.120 ... (remaining 50686 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 16.130 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.007 0.203 6718 Z= 0.351 Angle : 0.892 12.268 9145 Z= 0.539 Chirality : 0.055 0.470 970 Planarity : 0.024 0.478 1173 Dihedral : 14.996 89.673 2531 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 1.02 % Allowed : 4.45 % Favored : 94.54 % Rotamer: Outliers : 3.61 % Allowed : 1.44 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.30), residues: 787 helix: 0.47 (0.27), residues: 382 sheet: 2.28 (0.76), residues: 44 loop : -1.69 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.016 0.002 TYR A 202 PHE 0.015 0.002 PHE B 377 TRP 0.036 0.002 TRP A 165 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 6702) covalent geometry : angle 0.86963 ( 9110) SS BOND : bond 0.00166 ( 7) SS BOND : angle 0.79480 ( 14) hydrogen bonds : bond 0.17913 ( 291) hydrogen bonds : angle 6.02221 ( 816) metal coordination : bond 0.20191 ( 2) link_NAG-ASN : bond 0.00727 ( 7) link_NAG-ASN : angle 4.23312 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 35 GLU cc_start: 0.7210 (mp0) cc_final: 0.6755 (mp0) REVERT: A 74 LYS cc_start: 0.7962 (tttt) cc_final: 0.7591 (ttmm) REVERT: A 75 GLU cc_start: 0.7659 (tp30) cc_final: 0.7113 (tp30) REVERT: A 88 ILE cc_start: 0.7881 (mt) cc_final: 0.7410 (mt) REVERT: A 129 THR cc_start: 0.8484 (m) cc_final: 0.8100 (p) REVERT: A 150 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 162 LEU cc_start: 0.8305 (tt) cc_final: 0.8092 (tp) REVERT: A 167 SER cc_start: 0.8779 (m) cc_final: 0.8411 (p) REVERT: A 168 TRP cc_start: 0.8543 (t-100) cc_final: 0.8329 (t-100) REVERT: A 182 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6956 (mt-10) REVERT: A 221 GLN cc_start: 0.7840 (tp40) cc_final: 0.7597 (tt0) REVERT: A 269 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6853 (p0) REVERT: A 270 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8121 (tpp) REVERT: A 363 LYS cc_start: 0.7443 (mttm) cc_final: 0.7160 (mmtm) REVERT: A 365 THR cc_start: 0.8502 (m) cc_final: 0.8293 (p) REVERT: A 382 ASP cc_start: 0.7981 (m-30) cc_final: 0.7775 (m-30) REVERT: A 406 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 441 LYS cc_start: 0.8679 (tttp) cc_final: 0.8477 (tttm) REVERT: A 465 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8213 (ttmm) REVERT: A 467 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 483 GLU cc_start: 0.7490 (tp30) cc_final: 0.7195 (tp30) REVERT: A 553 LYS cc_start: 0.8474 (tttt) cc_final: 0.8225 (tttp) REVERT: A 557 MET cc_start: 0.8447 (tmm) cc_final: 0.8090 (tmm) REVERT: B 438 SER cc_start: 0.8526 (p) cc_final: 0.8206 (p) outliers start: 25 outliers final: 8 residues processed: 217 average time/residue: 0.0865 time to fit residues: 24.6048 Evaluate side-chains 191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 371 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.0170 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 265 HIS A 290 ASN A 401 HIS A 580 ASN B 354 ASN B 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107350 restraints weight = 9664.594| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.30 r_work: 0.3217 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6718 Z= 0.251 Angle : 0.703 7.932 9145 Z= 0.360 Chirality : 0.048 0.225 970 Planarity : 0.006 0.058 1173 Dihedral : 7.225 57.548 1030 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.46 % Favored : 94.03 % Rotamer: Outliers : 3.17 % Allowed : 10.39 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.29), residues: 787 helix: 0.66 (0.27), residues: 378 sheet: 2.04 (0.73), residues: 45 loop : -1.68 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 493 TYR 0.026 0.002 TYR A 183 PHE 0.016 0.002 PHE B 429 TRP 0.020 0.002 TRP B 436 HIS 0.005 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 6702) covalent geometry : angle 0.68191 ( 9110) SS BOND : bond 0.00655 ( 7) SS BOND : angle 2.23590 ( 14) hydrogen bonds : bond 0.06626 ( 291) hydrogen bonds : angle 4.57237 ( 816) metal coordination : bond 0.00286 ( 2) link_NAG-ASN : bond 0.00904 ( 7) link_NAG-ASN : angle 3.18703 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8186 (tp30) cc_final: 0.7669 (tp30) REVERT: A 82 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7706 (mmt) REVERT: A 86 GLN cc_start: 0.7785 (mp10) cc_final: 0.7232 (mp10) REVERT: A 89 GLN cc_start: 0.8037 (mp-120) cc_final: 0.7739 (mp10) REVERT: A 129 THR cc_start: 0.8565 (m) cc_final: 0.8267 (p) REVERT: A 131 LYS cc_start: 0.8422 (tptt) cc_final: 0.8154 (mptt) REVERT: A 162 LEU cc_start: 0.8446 (tt) cc_final: 0.8240 (tp) REVERT: A 167 SER cc_start: 0.8781 (m) cc_final: 0.8419 (p) REVERT: A 221 GLN cc_start: 0.8269 (tp40) cc_final: 0.7918 (tt0) REVERT: A 269 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7116 (p0) REVERT: A 363 LYS cc_start: 0.7932 (mttm) cc_final: 0.7683 (mmtm) REVERT: A 382 ASP cc_start: 0.8232 (m-30) cc_final: 0.8019 (m-30) REVERT: A 394 ASN cc_start: 0.8185 (m-40) cc_final: 0.7974 (m-40) REVERT: A 400 PHE cc_start: 0.8096 (m-10) cc_final: 0.7866 (m-80) REVERT: A 467 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7877 (mm-30) REVERT: A 534 LYS cc_start: 0.8226 (mptt) cc_final: 0.7906 (mptt) REVERT: A 557 MET cc_start: 0.8581 (tmm) cc_final: 0.8173 (tmm) REVERT: B 347 PHE cc_start: 0.8479 (m-80) cc_final: 0.8231 (m-80) REVERT: B 414 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8323 (mm-40) REVERT: B 438 SER cc_start: 0.8534 (p) cc_final: 0.8228 (p) REVERT: B 467 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.7021 (m-30) outliers start: 22 outliers final: 11 residues processed: 196 average time/residue: 0.0927 time to fit residues: 23.3447 Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 467 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 40 optimal weight: 0.0050 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109052 restraints weight = 9451.865| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.27 r_work: 0.3241 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6718 Z= 0.162 Angle : 0.612 9.160 9145 Z= 0.311 Chirality : 0.045 0.253 970 Planarity : 0.005 0.055 1173 Dihedral : 6.007 58.440 1018 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.94 % Favored : 95.55 % Rotamer: Outliers : 3.46 % Allowed : 14.43 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.30), residues: 787 helix: 1.07 (0.27), residues: 378 sheet: 1.93 (0.72), residues: 45 loop : -1.73 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 493 TYR 0.016 0.001 TYR A 202 PHE 0.011 0.001 PHE A 452 TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6702) covalent geometry : angle 0.58981 ( 9110) SS BOND : bond 0.00917 ( 7) SS BOND : angle 2.38229 ( 14) hydrogen bonds : bond 0.05342 ( 291) hydrogen bonds : angle 4.33014 ( 816) metal coordination : bond 0.00289 ( 2) link_NAG-ASN : bond 0.00624 ( 7) link_NAG-ASN : angle 2.91865 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7775 (m-30) cc_final: 0.7450 (m-30) REVERT: A 75 GLU cc_start: 0.8083 (tp30) cc_final: 0.7617 (tp30) REVERT: A 89 GLN cc_start: 0.7909 (mp-120) cc_final: 0.7558 (mp-120) REVERT: A 108 LEU cc_start: 0.8356 (mt) cc_final: 0.8133 (mt) REVERT: A 129 THR cc_start: 0.8547 (m) cc_final: 0.8260 (p) REVERT: A 131 LYS cc_start: 0.8380 (tptt) cc_final: 0.7741 (mptt) REVERT: A 167 SER cc_start: 0.8697 (m) cc_final: 0.8351 (p) REVERT: A 194 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7527 (t0) REVERT: A 221 GLN cc_start: 0.8192 (tp40) cc_final: 0.7834 (tp40) REVERT: A 233 ILE cc_start: 0.8165 (mt) cc_final: 0.7941 (tt) REVERT: A 269 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7140 (p0) REVERT: A 327 PHE cc_start: 0.8419 (t80) cc_final: 0.8209 (t80) REVERT: A 363 LYS cc_start: 0.7879 (mttm) cc_final: 0.7602 (mmtm) REVERT: A 394 ASN cc_start: 0.8147 (m-40) cc_final: 0.7902 (m-40) REVERT: A 467 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7835 (mm-30) REVERT: A 534 LYS cc_start: 0.8245 (mptt) cc_final: 0.7970 (mptt) REVERT: A 598 GLN cc_start: 0.8375 (tp40) cc_final: 0.7935 (tp40) REVERT: B 438 SER cc_start: 0.8522 (p) cc_final: 0.8217 (p) outliers start: 24 outliers final: 14 residues processed: 195 average time/residue: 0.0852 time to fit residues: 21.7007 Evaluate side-chains 188 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 68 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 0.0870 chunk 60 optimal weight: 0.0770 chunk 18 optimal weight: 0.3980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 154 ASN A 194 ASN A 388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108520 restraints weight = 9527.256| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.27 r_work: 0.3241 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6718 Z= 0.153 Angle : 0.614 13.485 9145 Z= 0.310 Chirality : 0.044 0.292 970 Planarity : 0.005 0.051 1173 Dihedral : 5.592 58.429 1013 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.19 % Favored : 95.43 % Rotamer: Outliers : 3.46 % Allowed : 16.02 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.30), residues: 787 helix: 1.15 (0.27), residues: 386 sheet: 1.68 (0.71), residues: 45 loop : -1.66 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.017 0.001 TYR A 183 PHE 0.010 0.001 PHE A 452 TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6702) covalent geometry : angle 0.59218 ( 9110) SS BOND : bond 0.00916 ( 7) SS BOND : angle 2.51074 ( 14) hydrogen bonds : bond 0.05126 ( 291) hydrogen bonds : angle 4.19602 ( 816) metal coordination : bond 0.00255 ( 2) link_NAG-ASN : bond 0.00566 ( 7) link_NAG-ASN : angle 2.80529 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7826 (m-30) cc_final: 0.7486 (m-30) REVERT: A 75 GLU cc_start: 0.8098 (tp30) cc_final: 0.7659 (tp30) REVERT: A 87 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7657 (mp0) REVERT: A 89 GLN cc_start: 0.7901 (mp-120) cc_final: 0.7552 (mp-120) REVERT: A 131 LYS cc_start: 0.8178 (tptt) cc_final: 0.7882 (mptt) REVERT: A 152 MET cc_start: 0.8148 (mmm) cc_final: 0.7474 (mtp) REVERT: A 167 SER cc_start: 0.8694 (m) cc_final: 0.8343 (p) REVERT: A 221 GLN cc_start: 0.8169 (tp40) cc_final: 0.7809 (tp40) REVERT: A 269 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7043 (p0) REVERT: A 363 LYS cc_start: 0.7857 (mttm) cc_final: 0.7567 (mmtm) REVERT: A 378 HIS cc_start: 0.8333 (m-70) cc_final: 0.8100 (m-70) REVERT: A 534 LYS cc_start: 0.8255 (mptt) cc_final: 0.7849 (mptt) REVERT: A 579 MET cc_start: 0.8700 (ptm) cc_final: 0.8457 (ptp) REVERT: A 598 GLN cc_start: 0.8319 (tp40) cc_final: 0.7870 (tp40) REVERT: B 377 PHE cc_start: 0.8404 (t80) cc_final: 0.8160 (t80) REVERT: B 438 SER cc_start: 0.8514 (p) cc_final: 0.8206 (p) outliers start: 24 outliers final: 14 residues processed: 189 average time/residue: 0.0835 time to fit residues: 20.6813 Evaluate side-chains 179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 45 optimal weight: 0.0470 chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 35 optimal weight: 0.1980 chunk 39 optimal weight: 0.0980 overall best weight: 0.2278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 98 GLN A 194 ASN A 388 GLN A 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.108157 restraints weight = 9529.640| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.28 r_work: 0.3176 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6718 Z= 0.166 Angle : 0.625 16.716 9145 Z= 0.314 Chirality : 0.044 0.261 970 Planarity : 0.005 0.050 1173 Dihedral : 5.531 58.342 1013 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.19 % Favored : 95.43 % Rotamer: Outliers : 4.18 % Allowed : 15.87 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.30), residues: 787 helix: 1.23 (0.27), residues: 387 sheet: 1.63 (0.72), residues: 45 loop : -1.61 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.017 0.001 TYR A 183 PHE 0.010 0.001 PHE A 452 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6702) covalent geometry : angle 0.60495 ( 9110) SS BOND : bond 0.01069 ( 7) SS BOND : angle 2.45712 ( 14) hydrogen bonds : bond 0.05311 ( 291) hydrogen bonds : angle 4.20316 ( 816) metal coordination : bond 0.00300 ( 2) link_NAG-ASN : bond 0.00529 ( 7) link_NAG-ASN : angle 2.73077 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7824 (m-30) cc_final: 0.7464 (m-30) REVERT: A 75 GLU cc_start: 0.8089 (tp30) cc_final: 0.7623 (tp30) REVERT: A 87 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7721 (mp0) REVERT: A 150 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7199 (tp30) REVERT: A 167 SER cc_start: 0.8663 (m) cc_final: 0.8200 (p) REVERT: A 221 GLN cc_start: 0.8136 (tp40) cc_final: 0.7779 (tt0) REVERT: A 231 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 233 ILE cc_start: 0.8450 (tt) cc_final: 0.8194 (tt) REVERT: A 269 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7134 (p0) REVERT: A 363 LYS cc_start: 0.7868 (mttm) cc_final: 0.7561 (mmtm) REVERT: A 378 HIS cc_start: 0.8228 (m-70) cc_final: 0.8000 (m-70) REVERT: A 394 ASN cc_start: 0.8072 (m110) cc_final: 0.7854 (m-40) REVERT: A 410 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 438 SER cc_start: 0.8542 (p) cc_final: 0.8228 (p) outliers start: 29 outliers final: 17 residues processed: 186 average time/residue: 0.0925 time to fit residues: 22.6291 Evaluate side-chains 187 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 19 optimal weight: 0.0980 chunk 43 optimal weight: 0.0170 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.0170 chunk 49 optimal weight: 0.1980 overall best weight: 0.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111371 restraints weight = 9644.785| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.31 r_work: 0.3265 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6718 Z= 0.117 Angle : 0.578 14.851 9145 Z= 0.289 Chirality : 0.042 0.225 970 Planarity : 0.005 0.054 1173 Dihedral : 5.208 59.316 1013 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.43 % Favored : 96.19 % Rotamer: Outliers : 2.31 % Allowed : 19.48 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.31), residues: 787 helix: 1.82 (0.28), residues: 368 sheet: 1.77 (0.70), residues: 44 loop : -1.36 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.010 0.001 TYR A 183 PHE 0.007 0.001 PHE A 452 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6702) covalent geometry : angle 0.55554 ( 9110) SS BOND : bond 0.00818 ( 7) SS BOND : angle 2.13737 ( 14) hydrogen bonds : bond 0.04011 ( 291) hydrogen bonds : angle 4.06110 ( 816) metal coordination : bond 0.00128 ( 2) link_NAG-ASN : bond 0.00515 ( 7) link_NAG-ASN : angle 2.90284 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7592 (tp30) cc_final: 0.6884 (tp30) REVERT: A 67 ASP cc_start: 0.7820 (m-30) cc_final: 0.7471 (m-30) REVERT: A 75 GLU cc_start: 0.8042 (tp30) cc_final: 0.7722 (tp30) REVERT: A 87 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7725 (mp0) REVERT: A 150 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7394 (tp30) REVERT: A 152 MET cc_start: 0.8082 (mmm) cc_final: 0.7679 (mtp) REVERT: A 154 ASN cc_start: 0.8603 (m-40) cc_final: 0.7936 (m110) REVERT: A 167 SER cc_start: 0.8726 (m) cc_final: 0.8325 (p) REVERT: A 192 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: A 231 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 233 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 269 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6950 (p0) REVERT: A 455 MET cc_start: 0.7455 (tmm) cc_final: 0.7217 (tmm) REVERT: A 509 ASP cc_start: 0.7987 (m-30) cc_final: 0.7748 (m-30) REVERT: B 438 SER cc_start: 0.8485 (p) cc_final: 0.8161 (p) outliers start: 16 outliers final: 10 residues processed: 194 average time/residue: 0.0805 time to fit residues: 20.8608 Evaluate side-chains 193 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0980 chunk 23 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.0270 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 overall best weight: 0.1238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110884 restraints weight = 9547.795| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.29 r_work: 0.3265 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6718 Z= 0.127 Angle : 0.578 14.308 9145 Z= 0.293 Chirality : 0.042 0.221 970 Planarity : 0.005 0.056 1173 Dihedral : 5.120 59.593 1013 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.94 % Favored : 95.68 % Rotamer: Outliers : 2.31 % Allowed : 21.21 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.31), residues: 787 helix: 1.92 (0.28), residues: 366 sheet: 1.82 (0.71), residues: 44 loop : -1.34 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.009 0.001 TYR A 613 PHE 0.010 0.001 PHE A 504 TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6702) covalent geometry : angle 0.56265 ( 9110) SS BOND : bond 0.00825 ( 7) SS BOND : angle 2.13274 ( 14) hydrogen bonds : bond 0.04364 ( 291) hydrogen bonds : angle 3.99980 ( 816) metal coordination : bond 0.00550 ( 2) link_NAG-ASN : bond 0.00547 ( 7) link_NAG-ASN : angle 2.30833 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7501 (tp30) cc_final: 0.6812 (tp30) REVERT: A 67 ASP cc_start: 0.7820 (m-30) cc_final: 0.7484 (m-30) REVERT: A 75 GLU cc_start: 0.8066 (tp30) cc_final: 0.7737 (tp30) REVERT: A 87 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7705 (mp0) REVERT: A 150 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7378 (tp30) REVERT: A 152 MET cc_start: 0.8092 (mmm) cc_final: 0.7639 (mtp) REVERT: A 154 ASN cc_start: 0.8554 (m-40) cc_final: 0.7892 (m110) REVERT: A 167 SER cc_start: 0.8716 (m) cc_final: 0.8358 (p) REVERT: A 192 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7737 (mtm-85) REVERT: A 231 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 233 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8210 (tt) REVERT: A 269 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6971 (p0) REVERT: A 270 MET cc_start: 0.8427 (tpp) cc_final: 0.8102 (tpp) REVERT: A 406 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 465 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8313 (ttmm) REVERT: B 438 SER cc_start: 0.8474 (p) cc_final: 0.8163 (p) outliers start: 16 outliers final: 12 residues processed: 184 average time/residue: 0.0877 time to fit residues: 21.2152 Evaluate side-chains 189 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 467 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 54 optimal weight: 0.0870 chunk 50 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108027 restraints weight = 9574.575| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.30 r_work: 0.3217 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6718 Z= 0.206 Angle : 0.645 14.526 9145 Z= 0.327 Chirality : 0.045 0.237 970 Planarity : 0.005 0.056 1173 Dihedral : 5.404 59.636 1013 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.81 % Favored : 95.81 % Rotamer: Outliers : 2.74 % Allowed : 21.93 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 787 helix: 1.56 (0.27), residues: 380 sheet: 1.57 (0.72), residues: 45 loop : -1.55 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.017 0.001 TYR A 202 PHE 0.012 0.001 PHE A 452 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 6702) covalent geometry : angle 0.62267 ( 9110) SS BOND : bond 0.00940 ( 7) SS BOND : angle 2.30902 ( 14) hydrogen bonds : bond 0.05780 ( 291) hydrogen bonds : angle 4.12398 ( 816) metal coordination : bond 0.00432 ( 2) link_NAG-ASN : bond 0.00449 ( 7) link_NAG-ASN : angle 3.08223 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7819 (m-30) cc_final: 0.7490 (m-30) REVERT: A 75 GLU cc_start: 0.8106 (tp30) cc_final: 0.7673 (tp30) REVERT: A 131 LYS cc_start: 0.8412 (tptt) cc_final: 0.8079 (tptt) REVERT: A 150 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7304 (tp30) REVERT: A 152 MET cc_start: 0.8116 (mmm) cc_final: 0.7561 (mtp) REVERT: A 154 ASN cc_start: 0.8539 (m-40) cc_final: 0.7826 (m110) REVERT: A 167 SER cc_start: 0.8706 (m) cc_final: 0.8293 (p) REVERT: A 192 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7782 (mtm-85) REVERT: A 221 GLN cc_start: 0.8162 (tp40) cc_final: 0.7860 (tt0) REVERT: A 231 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 233 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8286 (tt) REVERT: A 269 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7049 (p0) REVERT: A 270 MET cc_start: 0.8472 (tpp) cc_final: 0.8139 (tpp) REVERT: A 280 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (m) REVERT: A 332 MET cc_start: 0.8551 (ptm) cc_final: 0.8302 (ttp) REVERT: A 410 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 465 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8379 (ttmm) REVERT: B 438 SER cc_start: 0.8553 (p) cc_final: 0.8233 (p) outliers start: 19 outliers final: 11 residues processed: 176 average time/residue: 0.0878 time to fit residues: 20.1589 Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 56 optimal weight: 0.0020 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.0070 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 1 optimal weight: 0.3980 chunk 42 optimal weight: 0.1980 chunk 40 optimal weight: 0.0970 overall best weight: 0.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110502 restraints weight = 9605.930| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.30 r_work: 0.3260 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6718 Z= 0.130 Angle : 0.593 13.907 9145 Z= 0.301 Chirality : 0.043 0.221 970 Planarity : 0.005 0.056 1173 Dihedral : 5.199 59.042 1013 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.81 % Favored : 95.81 % Rotamer: Outliers : 2.02 % Allowed : 22.80 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.31), residues: 787 helix: 1.85 (0.27), residues: 372 sheet: 1.58 (0.72), residues: 45 loop : -1.35 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.017 0.001 TYR A 202 PHE 0.011 0.001 PHE A 504 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6702) covalent geometry : angle 0.57762 ( 9110) SS BOND : bond 0.00792 ( 7) SS BOND : angle 2.10573 ( 14) hydrogen bonds : bond 0.04517 ( 291) hydrogen bonds : angle 4.03835 ( 816) metal coordination : bond 0.00170 ( 2) link_NAG-ASN : bond 0.00491 ( 7) link_NAG-ASN : angle 2.30572 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7537 (tp30) cc_final: 0.6845 (tp30) REVERT: A 67 ASP cc_start: 0.7807 (m-30) cc_final: 0.7478 (m-30) REVERT: A 75 GLU cc_start: 0.8033 (tp30) cc_final: 0.7701 (tp30) REVERT: A 150 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7338 (tp30) REVERT: A 152 MET cc_start: 0.8106 (mmm) cc_final: 0.7620 (mtp) REVERT: A 154 ASN cc_start: 0.8513 (m-40) cc_final: 0.7811 (m110) REVERT: A 167 SER cc_start: 0.8695 (m) cc_final: 0.8278 (p) REVERT: A 192 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7740 (mtm-85) REVERT: A 231 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7723 (mm-30) REVERT: A 233 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8176 (tt) REVERT: A 269 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6964 (p0) REVERT: A 270 MET cc_start: 0.8421 (tpp) cc_final: 0.8094 (tpp) REVERT: A 406 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 410 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 465 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8357 (ttmm) REVERT: B 438 SER cc_start: 0.8515 (p) cc_final: 0.8196 (p) outliers start: 14 outliers final: 9 residues processed: 177 average time/residue: 0.0829 time to fit residues: 19.2618 Evaluate side-chains 175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 39 optimal weight: 0.0570 chunk 76 optimal weight: 0.0970 chunk 30 optimal weight: 0.0980 chunk 38 optimal weight: 0.0870 chunk 47 optimal weight: 0.4980 overall best weight: 0.0830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111914 restraints weight = 9507.050| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.30 r_work: 0.3283 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6718 Z= 0.118 Angle : 0.570 13.521 9145 Z= 0.290 Chirality : 0.042 0.210 970 Planarity : 0.005 0.057 1173 Dihedral : 4.887 57.549 1013 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.68 % Favored : 95.93 % Rotamer: Outliers : 1.88 % Allowed : 22.66 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.31), residues: 787 helix: 2.05 (0.28), residues: 365 sheet: 1.87 (0.71), residues: 44 loop : -1.32 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.017 0.001 TYR A 202 PHE 0.008 0.001 PHE A 452 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6702) covalent geometry : angle 0.55735 ( 9110) SS BOND : bond 0.00745 ( 7) SS BOND : angle 2.05023 ( 14) hydrogen bonds : bond 0.04038 ( 291) hydrogen bonds : angle 3.96205 ( 816) metal coordination : bond 0.00114 ( 2) link_NAG-ASN : bond 0.00339 ( 7) link_NAG-ASN : angle 1.94591 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7550 (tt0) cc_final: 0.7308 (tt0) REVERT: A 23 GLU cc_start: 0.7449 (tp30) cc_final: 0.6796 (tp30) REVERT: A 67 ASP cc_start: 0.7748 (m-30) cc_final: 0.7416 (m-30) REVERT: A 75 GLU cc_start: 0.8033 (tp30) cc_final: 0.7764 (tp30) REVERT: A 150 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7352 (tp30) REVERT: A 152 MET cc_start: 0.8085 (mmm) cc_final: 0.7595 (mtp) REVERT: A 154 ASN cc_start: 0.8487 (m-40) cc_final: 0.7797 (m110) REVERT: A 167 SER cc_start: 0.8673 (m) cc_final: 0.8232 (p) REVERT: A 192 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7755 (mtm-85) REVERT: A 231 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 233 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8194 (tt) REVERT: A 270 MET cc_start: 0.8381 (tpp) cc_final: 0.8078 (tpp) REVERT: A 360 MET cc_start: 0.7866 (ttp) cc_final: 0.7567 (ttm) REVERT: A 406 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 465 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8361 (ttmm) REVERT: B 438 SER cc_start: 0.8491 (p) cc_final: 0.8173 (p) outliers start: 13 outliers final: 10 residues processed: 181 average time/residue: 0.0850 time to fit residues: 20.2144 Evaluate side-chains 182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.0970 chunk 48 optimal weight: 0.0570 chunk 52 optimal weight: 0.0050 chunk 24 optimal weight: 0.0570 chunk 75 optimal weight: 0.0170 chunk 36 optimal weight: 0.0980 chunk 53 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 0.0570 chunk 67 optimal weight: 0.0470 overall best weight: 0.0366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 360 ASN B 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114970 restraints weight = 9577.452| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.32 r_work: 0.3326 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6718 Z= 0.111 Angle : 0.557 13.041 9145 Z= 0.283 Chirality : 0.041 0.204 970 Planarity : 0.005 0.057 1173 Dihedral : 4.640 55.035 1013 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.94 % Favored : 95.81 % Rotamer: Outliers : 1.30 % Allowed : 23.38 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.31), residues: 787 helix: 2.17 (0.28), residues: 364 sheet: 1.76 (0.71), residues: 44 loop : -1.23 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.016 0.001 TYR A 202 PHE 0.009 0.001 PHE A 504 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6702) covalent geometry : angle 0.54618 ( 9110) SS BOND : bond 0.00682 ( 7) SS BOND : angle 1.91928 ( 14) hydrogen bonds : bond 0.03512 ( 291) hydrogen bonds : angle 3.90294 ( 816) metal coordination : bond 0.00139 ( 2) link_NAG-ASN : bond 0.00367 ( 7) link_NAG-ASN : angle 1.75315 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2331.07 seconds wall clock time: 40 minutes 38.11 seconds (2438.11 seconds total)