Starting phenix.real_space_refine on Thu Jul 2 05:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r12_14228/07_2026/7r12_14228.cif" } resolution = 3.3 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= 0.002 sd= 0.089 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 39 5.16 5 C 4383 2.51 5 N 1130 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6858 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1972 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Time building chain proxies: 1.38, per 1000 atoms: 0.20 Number of scatterers: 6858 At special positions: 0 Unit cell: (75.46, 98.098, 139.062, 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 39 16.00 O 1305 8.00 N 1130 7.00 C 4383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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 A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 103 " " NAG D 905 " - " ASN D 546 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 333.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 52.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.441A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 4.067A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.642A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.763A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.523A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.556A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.594A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.059A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.704A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.036A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.700A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.618A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.970A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.547A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.602A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.543A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.533A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.964A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 4.081A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.622A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.617A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.696A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.862A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.525A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.752A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.199A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.287A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.643A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 301 hydrogen bonds defined for protein. 846 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: 0.76 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2194 1.34 - 1.46: 1719 1.46 - 1.58: 3068 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 7041 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 7036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 9391 1.72 - 3.44: 152 3.44 - 5.15: 20 5.15 - 6.87: 2 6.87 - 8.59: 1 Bond angle restraints: 9566 Sorted by residual: angle pdb=" C ASN D 90 " pdb=" N LEU D 91 " pdb=" CA LEU D 91 " ideal model delta sigma weight residual 121.54 126.61 -5.07 1.91e+00 2.74e-01 7.05e+00 angle pdb=" C LEU D 423 " pdb=" N LEU D 424 " pdb=" CA LEU D 424 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 7.00e+00 angle pdb=" CA LEU A 546 " pdb=" CB LEU A 546 " pdb=" CG LEU A 546 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" N ILE D 421 " pdb=" CA ILE D 421 " pdb=" C ILE D 421 " ideal model delta sigma weight residual 110.42 112.54 -2.12 9.60e-01 1.09e+00 4.87e+00 angle pdb=" N ASP D 427 " pdb=" CA ASP D 427 " pdb=" C ASP D 427 " ideal model delta sigma weight residual 110.88 108.11 2.77 1.28e+00 6.10e-01 4.68e+00 ... (remaining 9561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3712 17.55 - 35.10: 330 35.10 - 52.65: 60 52.65 - 70.20: 10 70.20 - 87.75: 4 Dihedral angle restraints: 4116 sinusoidal: 1661 harmonic: 2455 Sorted by residual: dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -119.56 33.56 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 123.28 -30.28 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA CYS D 344 " pdb=" C CYS D 344 " pdb=" N HIS D 345 " pdb=" CA HIS D 345 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 604 0.030 - 0.060: 300 0.060 - 0.089: 67 0.089 - 0.119: 55 0.119 - 0.149: 6 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" C1 NAG D 904 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D 904 " pdb=" O5 NAG D 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1029 not shown) Planarity restraints: 1235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO D 146 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO D 235 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 578 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 579 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " 0.017 5.00e-02 4.00e+02 ... (remaining 1232 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 133 2.71 - 3.26: 6429 3.26 - 3.80: 10119 3.80 - 4.35: 13356 4.35 - 4.90: 23311 Nonbonded interactions: 53348 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 901 " model vdw 2.211 2.230 nonbonded pdb=" O ARG A 408 " pdb=" NE2 GLN A 414 " model vdw 2.257 3.120 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.308 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.325 3.040 ... (remaining 53343 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: 3.220 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.790 Find NCS groups from input model: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7057 Z= 0.156 Angle : 0.568 9.935 9600 Z= 0.287 Chirality : 0.041 0.149 1032 Planarity : 0.004 0.050 1229 Dihedral : 13.542 87.747 2514 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.39 (0.29), residues: 831 helix: 1.22 (0.28), residues: 374 sheet: 0.95 (0.60), residues: 70 loop : -0.81 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.021 0.001 TYR D 199 PHE 0.011 0.001 PHE D 308 TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 7041) covalent geometry : angle 0.54902 / 0.28 ( 9566) SS BOND : bond 0.00240 / 0.16 ( 8) SS BOND : angle 0.70262 / 0.42 ( 16) hydrogen bonds : bond 0.13672 / 8.33 ( 301) hydrogen bonds : angle 5.46514 / 3.93 ( 846) metal coordination : bond 0.00301 / 0.15 ( 2) link_NAG-ASN : bond 0.00808 / 0.40 ( 6) link_NAG-ASN : angle 3.41144 / 2.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.200 Fit side-chains REVERT: D 160 GLU cc_start: 0.6626 (tt0) cc_final: 0.6374 (tt0) REVERT: D 470 LYS cc_start: 0.7909 (mttt) cc_final: 0.7490 (mmtm) REVERT: A 420 ASP cc_start: 0.8333 (m-30) cc_final: 0.7965 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0721 time to fit residues: 9.2838 Evaluate side-chains 79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.153299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.123791 restraints weight = 7218.030| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.35 r_work: 0.2885 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7057 Z= 0.152 Angle : 0.554 10.827 9600 Z= 0.276 Chirality : 0.042 0.161 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.158 17.392 906 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.35 % Allowed : 4.47 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 1.33 (0.28), residues: 383 sheet: 0.96 (0.60), residues: 70 loop : -0.72 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.020 0.002 TYR D 183 PHE 0.014 0.001 PHE D 327 TRP 0.008 0.001 TRP D 566 HIS 0.003 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 7041) covalent geometry : angle 0.53080 / 0.27 ( 9566) SS BOND : bond 0.00263 / 0.16 ( 8) SS BOND : angle 0.86673 / 0.52 ( 16) hydrogen bonds : bond 0.05173 / 3.54 ( 301) hydrogen bonds : angle 4.46278 / 3.21 ( 846) metal coordination : bond 0.00336 / 0.17 ( 2) link_NAG-ASN : bond 0.00707 / 0.36 ( 6) link_NAG-ASN : angle 3.61465 / 2.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.282 Fit side-chains REVERT: D 160 GLU cc_start: 0.7257 (tt0) cc_final: 0.6821 (tt0) REVERT: D 470 LYS cc_start: 0.8078 (mttt) cc_final: 0.7444 (mmtm) REVERT: A 405 ASP cc_start: 0.8251 (m-30) cc_final: 0.8047 (m-30) REVERT: A 420 ASP cc_start: 0.8852 (m-30) cc_final: 0.8293 (m-30) outliers start: 10 outliers final: 8 residues processed: 87 average time/residue: 0.0634 time to fit residues: 7.8913 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 54 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 60 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 58 ASN A 354 ASN A 414 GLN 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 = 0.157320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129843 restraints weight = 7199.958| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.33 r_work: 0.2969 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7057 Z= 0.096 Angle : 0.466 6.275 9600 Z= 0.238 Chirality : 0.040 0.205 1032 Planarity : 0.004 0.047 1229 Dihedral : 3.832 14.970 906 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.08 % Allowed : 6.90 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.92 (0.29), residues: 831 helix: 1.57 (0.28), residues: 385 sheet: 0.82 (0.60), residues: 70 loop : -0.39 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.018 0.001 TYR D 183 PHE 0.007 0.001 PHE D 308 TRP 0.008 0.001 TRP D 168 HIS 0.003 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 7041) covalent geometry : angle 0.45979 / 0.24 ( 9566) SS BOND : bond 0.00377 / 0.28 ( 8) SS BOND : angle 1.69117 / 0.90 ( 16) hydrogen bonds : bond 0.03882 / 2.69 ( 301) hydrogen bonds : angle 4.23292 / 3.04 ( 846) metal coordination : bond 0.00141 / 0.07 ( 2) link_NAG-ASN : bond 0.00256 / 0.13 ( 6) link_NAG-ASN : angle 1.02765 / 0.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.252 Fit side-chains REVERT: D 160 GLU cc_start: 0.7172 (tt0) cc_final: 0.6714 (tt0) REVERT: D 175 GLN cc_start: 0.7186 (mt0) cc_final: 0.6790 (mt0) REVERT: D 462 MET cc_start: 0.8394 (mtt) cc_final: 0.8086 (mtm) REVERT: D 470 LYS cc_start: 0.7979 (mttt) cc_final: 0.7359 (mmtm) REVERT: A 420 ASP cc_start: 0.8738 (m-30) cc_final: 0.8300 (m-30) outliers start: 8 outliers final: 6 residues processed: 93 average time/residue: 0.0734 time to fit residues: 9.4975 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain A residue 354 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 35 optimal weight: 0.0570 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.0370 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.155322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.128499 restraints weight = 7234.068| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.27 r_work: 0.2974 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7057 Z= 0.122 Angle : 0.500 7.511 9600 Z= 0.254 Chirality : 0.041 0.251 1032 Planarity : 0.004 0.048 1229 Dihedral : 3.880 15.530 906 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.76 % Allowed : 7.71 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.29), residues: 831 helix: 1.58 (0.28), residues: 385 sheet: 0.94 (0.60), residues: 70 loop : -0.38 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 204 TYR 0.015 0.001 TYR D 183 PHE 0.011 0.001 PHE D 327 TRP 0.007 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 7041) covalent geometry : angle 0.49079 / 0.25 ( 9566) SS BOND : bond 0.00659 / 0.49 ( 8) SS BOND : angle 2.14679 / 1.28 ( 16) hydrogen bonds : bond 0.04346 / 2.99 ( 301) hydrogen bonds : angle 4.20658 / 3.02 ( 846) metal coordination : bond 0.00225 / 0.11 ( 2) link_NAG-ASN : bond 0.00152 / 0.08 ( 6) link_NAG-ASN : angle 1.20038 / 0.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.179 Fit side-chains REVERT: D 160 GLU cc_start: 0.7145 (tt0) cc_final: 0.6707 (tt0) REVERT: D 175 GLN cc_start: 0.7230 (mt0) cc_final: 0.6889 (mt0) REVERT: D 470 LYS cc_start: 0.7979 (mttt) cc_final: 0.7376 (mmtm) REVERT: A 405 ASP cc_start: 0.7903 (m-30) cc_final: 0.7687 (m-30) REVERT: A 420 ASP cc_start: 0.8724 (m-30) cc_final: 0.8293 (m-30) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.0656 time to fit residues: 8.2861 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 58 optimal weight: 0.0170 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.0030 chunk 32 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.0170 overall best weight: 0.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 397 ASN D 522 GLN D 552 GLN A 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.181900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.172155 restraints weight = 7071.113| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 0.44 r_work: 0.3345 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 7057 Z= 0.087 Angle : 0.451 12.188 9600 Z= 0.226 Chirality : 0.039 0.260 1032 Planarity : 0.003 0.047 1229 Dihedral : 3.491 13.564 906 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.68 % Allowed : 10.28 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 831 helix: 1.85 (0.28), residues: 378 sheet: 0.87 (0.59), residues: 78 loop : -0.24 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.013 0.001 TYR D 183 PHE 0.005 0.001 PHE A 453 TRP 0.012 0.001 TRP D 168 HIS 0.002 0.000 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 7041) covalent geometry : angle 0.44020 / 0.22 ( 9566) SS BOND : bond 0.00648 / 0.49 ( 8) SS BOND : angle 2.24861 / 1.34 ( 16) hydrogen bonds : bond 0.03064 / 2.13 ( 301) hydrogen bonds : angle 3.93092 / 2.84 ( 846) metal coordination : bond 0.00050 / 0.02 ( 2) link_NAG-ASN : bond 0.00188 / 0.10 ( 6) link_NAG-ASN : angle 0.99113 / 0.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.247 Fit side-chains REVERT: D 160 GLU cc_start: 0.6967 (tt0) cc_final: 0.6532 (tt0) REVERT: D 470 LYS cc_start: 0.7875 (mttt) cc_final: 0.7329 (mmtm) REVERT: A 420 ASP cc_start: 0.8465 (m-30) cc_final: 0.8080 (m-30) outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.0767 time to fit residues: 9.9888 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 68 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 522 GLN D 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.155217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.127978 restraints weight = 7307.198| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.25 r_work: 0.2966 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 7057 Z= 0.129 Angle : 0.525 13.839 9600 Z= 0.262 Chirality : 0.041 0.269 1032 Planarity : 0.004 0.049 1229 Dihedral : 3.788 13.964 906 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.08 % Allowed : 10.55 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.30), residues: 831 helix: 1.74 (0.28), residues: 385 sheet: 1.31 (0.63), residues: 71 loop : -0.33 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 204 TYR 0.019 0.001 TYR D 50 PHE 0.014 0.001 PHE D 327 TRP 0.008 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 7041) covalent geometry : angle 0.51474 / 0.26 ( 9566) SS BOND : bond 0.00632 / 0.47 ( 8) SS BOND : angle 2.20959 / 1.35 ( 16) hydrogen bonds : bond 0.04390 / 3.01 ( 301) hydrogen bonds : angle 4.08446 / 2.95 ( 846) metal coordination : bond 0.00269 / 0.14 ( 2) link_NAG-ASN : bond 0.00148 / 0.08 ( 6) link_NAG-ASN : angle 1.32368 / 0.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.297 Fit side-chains REVERT: D 128 SER cc_start: 0.7566 (t) cc_final: 0.7245 (m) REVERT: D 160 GLU cc_start: 0.7183 (tt0) cc_final: 0.6716 (tt0) REVERT: D 175 GLN cc_start: 0.7027 (mt0) cc_final: 0.6728 (mt0) REVERT: D 470 LYS cc_start: 0.7948 (mttt) cc_final: 0.7344 (mmtm) REVERT: A 389 ASP cc_start: 0.7099 (m-30) cc_final: 0.6717 (p0) REVERT: A 405 ASP cc_start: 0.8030 (m-30) cc_final: 0.7698 (m-30) REVERT: A 420 ASP cc_start: 0.8732 (m-30) cc_final: 0.8346 (m-30) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.0705 time to fit residues: 8.4410 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.152744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.127701 restraints weight = 7199.854| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.16 r_work: 0.2951 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7057 Z= 0.160 Angle : 0.575 14.111 9600 Z= 0.282 Chirality : 0.042 0.274 1032 Planarity : 0.004 0.050 1229 Dihedral : 4.055 15.558 906 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.62 % Allowed : 10.01 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.89 (0.29), residues: 831 helix: 1.50 (0.28), residues: 390 sheet: 1.24 (0.63), residues: 71 loop : -0.49 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 204 TYR 0.018 0.002 TYR D 50 PHE 0.016 0.001 PHE D 327 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 ( 7041) covalent geometry : angle 0.56449 / 0.28 ( 9566) SS BOND : bond 0.00812 / 0.61 ( 8) SS BOND : angle 2.23886 / 1.34 ( 16) hydrogen bonds : bond 0.05039 / 3.45 ( 301) hydrogen bonds : angle 4.21670 / 3.04 ( 846) metal coordination : bond 0.00384 / 0.20 ( 2) link_NAG-ASN : bond 0.00190 / 0.10 ( 6) link_NAG-ASN : angle 1.54453 / 1.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.180 Fit side-chains REVERT: D 128 SER cc_start: 0.7741 (t) cc_final: 0.7436 (m) REVERT: D 160 GLU cc_start: 0.7124 (tt0) cc_final: 0.6769 (tt0) REVERT: D 175 GLN cc_start: 0.7153 (mt0) cc_final: 0.6821 (mt0) REVERT: A 420 ASP cc_start: 0.8731 (m-30) cc_final: 0.8254 (m-30) REVERT: A 546 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7112 (pt) outliers start: 12 outliers final: 10 residues processed: 91 average time/residue: 0.0580 time to fit residues: 7.4877 Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 546 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 51 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 = 0.151698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.122383 restraints weight = 7322.561| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.43 r_work: 0.3127 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 7057 Z= 0.181 Angle : 0.604 13.245 9600 Z= 0.297 Chirality : 0.044 0.270 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.209 16.430 906 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.03 % Allowed : 9.74 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.69 (0.29), residues: 831 helix: 1.33 (0.28), residues: 390 sheet: 1.15 (0.63), residues: 71 loop : -0.59 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.023 0.002 TYR D 50 PHE 0.017 0.002 PHE D 327 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 ( 7041) covalent geometry : angle 0.58933 / 0.29 ( 9566) SS BOND : bond 0.00760 / 0.57 ( 8) SS BOND : angle 2.20905 / 1.31 ( 16) hydrogen bonds : bond 0.05383 / 3.69 ( 301) hydrogen bonds : angle 4.27809 / 3.09 ( 846) metal coordination : bond 0.00445 / 0.23 ( 2) link_NAG-ASN : bond 0.00202 / 0.10 ( 6) link_NAG-ASN : angle 2.31525 / 1.53 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: D 128 SER cc_start: 0.7589 (t) cc_final: 0.7258 (m) REVERT: D 175 GLN cc_start: 0.7169 (mt0) cc_final: 0.6758 (mt0) REVERT: D 470 LYS cc_start: 0.8160 (mttt) cc_final: 0.7517 (mmtm) REVERT: D 568 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 420 ASP cc_start: 0.8825 (m-30) cc_final: 0.8349 (m-30) REVERT: A 546 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6833 (pt) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.0682 time to fit residues: 8.9062 Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 546 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN 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 = 0.151860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.123100 restraints weight = 7327.818| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.36 r_work: 0.2886 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 7057 Z= 0.173 Angle : 0.598 14.644 9600 Z= 0.293 Chirality : 0.043 0.270 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.236 17.099 906 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.89 % Allowed : 10.01 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.29), residues: 831 helix: 1.34 (0.28), residues: 387 sheet: 1.09 (0.63), residues: 70 loop : -0.59 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.015 0.002 TYR D 50 PHE 0.016 0.002 PHE D 327 TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.17 ( 7041) covalent geometry : angle 0.58460 / 0.29 ( 9566) SS BOND : bond 0.00803 / 0.60 ( 8) SS BOND : angle 2.20472 / 1.33 ( 16) hydrogen bonds : bond 0.05271 / 3.60 ( 301) hydrogen bonds : angle 4.28815 / 3.10 ( 846) metal coordination : bond 0.00421 / 0.21 ( 2) link_NAG-ASN : bond 0.00248 / 0.12 ( 6) link_NAG-ASN : angle 2.14456 / 1.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: D 128 SER cc_start: 0.7658 (t) cc_final: 0.7316 (m) REVERT: D 175 GLN cc_start: 0.7103 (mt0) cc_final: 0.6825 (mt0) REVERT: D 470 LYS cc_start: 0.8120 (mttt) cc_final: 0.7519 (mmtm) REVERT: D 568 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 420 ASP cc_start: 0.8797 (m-30) cc_final: 0.8317 (m-30) REVERT: A 546 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7024 (pt) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.0668 time to fit residues: 8.6098 Evaluate side-chains 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.0000 chunk 15 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 81 optimal weight: 4.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.154023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.126027 restraints weight = 7233.737| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.28 r_work: 0.2939 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7057 Z= 0.127 Angle : 0.547 14.014 9600 Z= 0.270 Chirality : 0.041 0.248 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.043 16.790 906 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.22 % Allowed : 10.83 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.87 (0.29), residues: 831 helix: 1.52 (0.28), residues: 384 sheet: 1.18 (0.64), residues: 70 loop : -0.50 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.015 0.001 TYR D 50 PHE 0.011 0.001 PHE D 327 TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7041) covalent geometry : angle 0.53672 / 0.27 ( 9566) SS BOND : bond 0.00706 / 0.53 ( 8) SS BOND : angle 2.01083 / 1.19 ( 16) hydrogen bonds : bond 0.04558 / 3.14 ( 301) hydrogen bonds : angle 4.15916 / 3.01 ( 846) metal coordination : bond 0.00244 / 0.12 ( 2) link_NAG-ASN : bond 0.00188 / 0.10 ( 6) link_NAG-ASN : angle 1.77556 / 1.18 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.153 Fit side-chains REVERT: D 128 SER cc_start: 0.7641 (t) cc_final: 0.7344 (m) REVERT: D 160 GLU cc_start: 0.7164 (tt0) cc_final: 0.6777 (tt0) REVERT: D 175 GLN cc_start: 0.7142 (mt0) cc_final: 0.6822 (mt0) REVERT: D 470 LYS cc_start: 0.8054 (mttt) cc_final: 0.7439 (mmtm) REVERT: A 420 ASP cc_start: 0.8769 (m-30) cc_final: 0.8319 (m-30) REVERT: A 546 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7009 (pt) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.0713 time to fit residues: 8.7714 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 63 optimal weight: 0.1980 chunk 75 optimal weight: 0.3980 chunk 18 optimal weight: 0.0030 overall best weight: 0.1526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.157850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.131500 restraints weight = 7179.256| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.25 r_work: 0.3185 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 7057 Z= 0.097 Angle : 0.506 13.607 9600 Z= 0.250 Chirality : 0.040 0.229 1032 Planarity : 0.004 0.048 1229 Dihedral : 3.765 15.227 906 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.08 % Allowed : 11.10 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.30), residues: 831 helix: 1.75 (0.28), residues: 379 sheet: 1.07 (0.58), residues: 80 loop : -0.39 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 460 TYR 0.013 0.001 TYR D 50 PHE 0.007 0.001 PHE D 308 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 7041) covalent geometry : angle 0.49755 / 0.25 ( 9566) SS BOND : bond 0.00646 / 0.49 ( 8) SS BOND : angle 1.81721 / 1.06 ( 16) hydrogen bonds : bond 0.03752 / 2.59 ( 301) hydrogen bonds : angle 3.99905 / 2.89 ( 846) metal coordination : bond 0.00102 / 0.05 ( 2) link_NAG-ASN : bond 0.00179 / 0.09 ( 6) link_NAG-ASN : angle 1.45888 / 0.96 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.11 seconds wall clock time: 27 minutes 4.27 seconds (1624.27 seconds total)