Starting phenix.real_space_refine on Thu Mar 5 12:26:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bh2_12186/03_2026/7bh2_12186_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bh2_12186/03_2026/7bh2_12186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bh2_12186/03_2026/7bh2_12186_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bh2_12186/03_2026/7bh2_12186_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bh2_12186/03_2026/7bh2_12186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bh2_12186/03_2026/7bh2_12186.map" } resolution = 3.0 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= 0.026 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: 10 Type Number sf(0) Gaussians K 2 8.98 5 P 1 5.49 5 Mg 1 5.21 5 S 62 5.16 5 Be 1 3.05 5 C 7004 2.51 5 N 1824 2.21 5 O 1979 1.98 5 F 3 1.80 5 H 11172 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22049 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 10201 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "C" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2879 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 430 Classifications: {'peptide': 29} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 28} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, '9Y0': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 3.69, per 1000 atoms: 0.17 Number of scatterers: 22049 At special positions: 0 Unit cell: (75.53, 99.268, 176.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) K 2 19.00 S 62 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 1979 8.00 N 1824 7.00 C 7004 6.00 Be 1 4.00 H 11172 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 642.7 milliseconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 62.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 Proline residue: A 22 - end of helix removed outlier: 3.821A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.540A pdb=" N ILE A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 removed outlier: 3.514A pdb=" N ASP A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.609A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.459A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.654A pdb=" N ASN A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.629A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 305 removed outlier: 3.837A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.610A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.623A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.722A pdb=" N SER A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 444 " --> pdb=" O GLY A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.098A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 508 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 523 through 549 removed outlier: 4.096A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Proline residue: A 545 - end of helix removed outlier: 3.582A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.615A pdb=" N VAL B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 61 through 88 removed outlier: 3.993A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 246 removed outlier: 4.446A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 4.120A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.518A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.597A pdb=" N GLY B 268 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.002A pdb=" N GLU B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.678A pdb=" N GLN B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.102A pdb=" N ARG B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.712A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 591 removed outlier: 3.888A pdb=" N HIS B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 595 removed outlier: 3.877A pdb=" N PHE B 595 " --> pdb=" O PRO B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 612 through 638 removed outlier: 4.197A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix removed outlier: 3.605A pdb=" N LYS B 637 " --> pdb=" O PRO B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 680 removed outlier: 3.654A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.911A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.726A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.732A pdb=" N ASP C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 122 removed outlier: 4.070A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.690A pdb=" N GLY B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 176 " --> pdb=" O GLY B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 removed outlier: 4.317A pdb=" N ARG B 181 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.903A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY B 517 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AA8, first strand: chain 'B' and resid 321 through 323 removed outlier: 4.115A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.333A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.543A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 175 " --> pdb=" O GLN C 164 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1941 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: 5.26 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 11160 1.01 - 1.21: 14 1.21 - 1.41: 4309 1.41 - 1.61: 6635 1.61 - 1.81: 114 Bond restraints: 22232 Sorted by residual: bond pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" ND2 ASN B 624 " pdb="HD21 ASN B 624 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN B 624 " pdb="HD22 ASN B 624 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" F3 BEF B 803 " pdb="BE BEF B 803 " ideal model delta sigma weight residual 1.476 1.363 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" F2 BEF B 803 " pdb="BE BEF B 803 " ideal model delta sigma weight residual 1.476 1.365 0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 22227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 40268 5.62 - 11.25: 23 11.25 - 16.87: 3 16.87 - 22.49: 0 22.49 - 28.12: 3 Bond angle restraints: 40297 Sorted by residual: angle pdb=" CD GLN B 528 " pdb=" NE2 GLN B 528 " pdb="HE22 GLN B 528 " ideal model delta sigma weight residual 120.00 148.12 -28.12 3.00e+00 1.11e-01 8.78e+01 angle pdb="HE21 GLN B 528 " pdb=" NE2 GLN B 528 " pdb="HE22 GLN B 528 " ideal model delta sigma weight residual 120.00 94.29 25.71 3.00e+00 1.11e-01 7.35e+01 angle pdb=" CD GLN B 528 " pdb=" NE2 GLN B 528 " pdb="HE21 GLN B 528 " ideal model delta sigma weight residual 120.00 96.55 23.45 3.00e+00 1.11e-01 6.11e+01 angle pdb=" C12 9Y0 B 801 " pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 127.16 112.40 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " pdb=" C15 9Y0 B 801 " ideal model delta sigma weight residual 127.64 113.67 13.97 3.00e+00 1.11e-01 2.17e+01 ... (remaining 40292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 10046 34.37 - 68.73: 347 68.73 - 103.10: 9 103.10 - 137.46: 2 137.46 - 171.83: 1 Dihedral angle restraints: 10405 sinusoidal: 5729 harmonic: 4676 Sorted by residual: dihedral pdb=" N 9Y0 B 801 " pdb=" C3 9Y0 B 801 " pdb=" C4 9Y0 B 801 " pdb=" O1 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual 297.35 125.52 171.83 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " pdb=" C15 9Y0 B 801 " pdb=" C16 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual 127.88 -8.28 136.16 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA LEU A 124 " pdb=" C LEU A 124 " pdb=" N SER A 125 " pdb=" CA SER A 125 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 10402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1240 0.045 - 0.089: 440 0.089 - 0.134: 109 0.134 - 0.179: 15 0.179 - 0.223: 3 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CB THR B 677 " pdb=" CA THR B 677 " pdb=" OG1 THR B 677 " pdb=" CG2 THR B 677 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA PHE A 543 " pdb=" N PHE A 543 " pdb=" C PHE A 543 " pdb=" CB PHE A 543 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 1804 not shown) Planarity restraints: 3285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 B 801 " 0.148 2.00e-02 2.50e+03 3.29e-01 1.08e+03 pdb=" C13 9Y0 B 801 " -0.431 2.00e-02 2.50e+03 pdb=" C14 9Y0 B 801 " 0.446 2.00e-02 2.50e+03 pdb=" C15 9Y0 B 801 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 528 " -0.050 2.00e-02 2.50e+03 9.01e-02 1.22e+02 pdb=" CD GLN B 528 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN B 528 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN B 528 " 0.155 2.00e-02 2.50e+03 pdb="HE21 GLN B 528 " 0.037 2.00e-02 2.50e+03 pdb="HE22 GLN B 528 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 408 " -0.040 2.00e-02 2.50e+03 6.64e-02 6.61e+01 pdb=" CG ASN B 408 " 0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 408 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 408 " -0.111 2.00e-02 2.50e+03 pdb="HD21 ASN B 408 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN B 408 " 0.074 2.00e-02 2.50e+03 ... (remaining 3282 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.32: 5656 2.32 - 3.02: 61394 3.02 - 3.73: 80523 3.73 - 4.43: 126312 4.43 - 5.14: 198940 Nonbonded interactions: 472825 Sorted by model distance: nonbonded pdb=" O ASP B 329 " pdb=" H THR B 332 " model vdw 1.614 2.450 nonbonded pdb="HH22 ARG B 281 " pdb=" OE1 GLN B 567 " model vdw 1.619 2.450 nonbonded pdb="HH12 ARG B 475 " pdb=" OE1 GLU B 493 " model vdw 1.644 2.450 nonbonded pdb=" O VAL A 329 " pdb=" HG SER A 333 " model vdw 1.653 2.450 nonbonded pdb=" OD1 ASN B 387 " pdb="HH12 ARG B 394 " model vdw 1.679 2.450 ... (remaining 472820 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 20.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.009 0.204 11060 Z= 0.383 Angle : 0.852 14.760 15039 Z= 0.444 Chirality : 0.048 0.223 1807 Planarity : 0.010 0.329 1906 Dihedral : 13.527 171.828 3952 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.18 % Allowed : 8.55 % Favored : 91.28 % 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: -2.75 (0.19), residues: 1442 helix: -0.73 (0.16), residues: 844 sheet: -3.92 (0.37), residues: 106 loop : -3.16 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 281 TYR 0.026 0.003 TYR B 657 PHE 0.033 0.003 PHE A 109 TRP 0.012 0.002 TRP B 240 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00892 (11060) covalent geometry : angle 0.85234 (15039) hydrogen bonds : bond 0.13228 ( 661) hydrogen bonds : angle 6.00945 ( 1941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7302 (mmt) cc_final: 0.6908 (mpt) REVERT: A 55 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6141 (ptt-90) REVERT: A 112 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8113 (t0) REVERT: A 116 ARG cc_start: 0.7806 (mtp-110) cc_final: 0.7320 (ptm-80) REVERT: A 205 ASN cc_start: 0.7642 (p0) cc_final: 0.7131 (p0) REVERT: A 274 MET cc_start: 0.8441 (mmt) cc_final: 0.8197 (mmt) REVERT: A 408 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8371 (tttm) REVERT: B 138 ASP cc_start: 0.7451 (m-30) cc_final: 0.7040 (t70) REVERT: B 302 ASP cc_start: 0.7756 (m-30) cc_final: 0.7540 (m-30) REVERT: B 321 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5769 (pt0) REVERT: B 331 LYS cc_start: 0.7665 (tttt) cc_final: 0.7199 (ttpp) REVERT: B 383 MET cc_start: 0.8766 (ptp) cc_final: 0.8529 (ptt) REVERT: B 679 CYS cc_start: 0.7015 (m) cc_final: 0.6728 (m) REVERT: C 164 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7609 (mt0) REVERT: C 169 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8259 (mptt) REVERT: C 190 GLU cc_start: 0.6955 (mp0) cc_final: 0.6722 (mm-30) REVERT: D 1 MET cc_start: 0.5471 (mtm) cc_final: 0.4895 (mtm) outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 1.2505 time to fit residues: 186.8287 Evaluate side-chains 110 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 112 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 55 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 136 GLN A 252 ASN B 408 ASN B 426 GLN C 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.093113 restraints weight = 39092.287| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.17 r_work: 0.2976 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11060 Z= 0.136 Angle : 0.568 5.892 15039 Z= 0.300 Chirality : 0.039 0.163 1807 Planarity : 0.005 0.065 1906 Dihedral : 8.962 142.116 1573 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.06 % Allowed : 10.75 % Favored : 88.19 % 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: -1.08 (0.21), residues: 1442 helix: 0.65 (0.17), residues: 851 sheet: -3.57 (0.39), residues: 106 loop : -2.51 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 281 TYR 0.025 0.001 TYR A 381 PHE 0.016 0.001 PHE A 109 TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00296 (11060) covalent geometry : angle 0.56844 (15039) hydrogen bonds : bond 0.05435 ( 661) hydrogen bonds : angle 4.76781 ( 1941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7341 (mmt) cc_final: 0.7130 (mpt) REVERT: A 55 ARG cc_start: 0.7339 (ttp-110) cc_final: 0.6011 (ptt-90) REVERT: A 205 ASN cc_start: 0.7789 (p0) cc_final: 0.7345 (p0) REVERT: A 274 MET cc_start: 0.8473 (mmt) cc_final: 0.8221 (mmt) REVERT: A 378 SER cc_start: 0.7678 (t) cc_final: 0.7455 (m) REVERT: A 408 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8378 (tttm) REVERT: B 102 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7825 (ttmm) REVERT: B 138 ASP cc_start: 0.7716 (m-30) cc_final: 0.7302 (t0) REVERT: B 302 ASP cc_start: 0.8134 (m-30) cc_final: 0.7863 (m-30) REVERT: B 321 GLU cc_start: 0.6451 (mt-10) cc_final: 0.5707 (pt0) REVERT: B 331 LYS cc_start: 0.7588 (tttt) cc_final: 0.7109 (ttpp) REVERT: B 438 ARG cc_start: 0.7255 (ptt180) cc_final: 0.6949 (ptt90) REVERT: B 522 ASP cc_start: 0.8216 (m-30) cc_final: 0.7906 (m-30) REVERT: B 655 TRP cc_start: 0.7856 (m100) cc_final: 0.7452 (t-100) REVERT: C 164 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7393 (mt0) REVERT: C 169 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8185 (mptt) REVERT: D 1 MET cc_start: 0.5320 (mtm) cc_final: 0.4632 (mtm) outliers start: 12 outliers final: 5 residues processed: 125 average time/residue: 1.1004 time to fit residues: 150.0377 Evaluate side-chains 111 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 136 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092191 restraints weight = 39085.660| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.16 r_work: 0.2964 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11060 Z= 0.159 Angle : 0.543 5.992 15039 Z= 0.287 Chirality : 0.039 0.156 1807 Planarity : 0.005 0.054 1906 Dihedral : 8.105 92.270 1571 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.79 % Allowed : 11.81 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1442 helix: 1.15 (0.18), residues: 852 sheet: -3.30 (0.42), residues: 106 loop : -2.34 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.025 0.002 TYR A 381 PHE 0.017 0.001 PHE A 109 TRP 0.007 0.001 TRP B 71 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00376 (11060) covalent geometry : angle 0.54317 (15039) hydrogen bonds : bond 0.05261 ( 661) hydrogen bonds : angle 4.56219 ( 1941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7293 (ttp-110) cc_final: 0.5984 (ptt-90) REVERT: A 205 ASN cc_start: 0.7723 (p0) cc_final: 0.7259 (p0) REVERT: A 274 MET cc_start: 0.8465 (mmt) cc_final: 0.8202 (mmt) REVERT: A 408 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8380 (tttm) REVERT: B 102 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8027 (ttmm) REVERT: B 138 ASP cc_start: 0.7743 (m-30) cc_final: 0.7334 (t0) REVERT: B 302 ASP cc_start: 0.8142 (m-30) cc_final: 0.7859 (m-30) REVERT: B 321 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5787 (pt0) REVERT: B 331 LYS cc_start: 0.7576 (tttt) cc_final: 0.7128 (ttpp) REVERT: B 655 TRP cc_start: 0.7887 (m100) cc_final: 0.7497 (t-100) REVERT: C 119 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: C 164 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7474 (mt0) REVERT: C 169 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8196 (mptt) REVERT: D 1 MET cc_start: 0.5343 (mtm) cc_final: 0.4653 (mtm) outliers start: 9 outliers final: 6 residues processed: 115 average time/residue: 1.1214 time to fit residues: 141.4915 Evaluate side-chains 113 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 119 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093160 restraints weight = 38421.219| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.15 r_work: 0.2988 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11060 Z= 0.130 Angle : 0.513 5.747 15039 Z= 0.270 Chirality : 0.038 0.147 1807 Planarity : 0.004 0.048 1906 Dihedral : 7.302 73.152 1571 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.97 % Allowed : 12.42 % Favored : 86.61 % 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: -0.12 (0.22), residues: 1442 helix: 1.44 (0.18), residues: 853 sheet: -3.09 (0.43), residues: 106 loop : -2.19 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 391 TYR 0.024 0.001 TYR A 381 PHE 0.014 0.001 PHE A 109 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00298 (11060) covalent geometry : angle 0.51300 (15039) hydrogen bonds : bond 0.04696 ( 661) hydrogen bonds : angle 4.38980 ( 1941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.5944 (ptt90) REVERT: A 116 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7319 (ptm-80) REVERT: A 205 ASN cc_start: 0.7671 (p0) cc_final: 0.7191 (p0) REVERT: A 274 MET cc_start: 0.8415 (mmt) cc_final: 0.8172 (mmt) REVERT: A 378 SER cc_start: 0.7679 (t) cc_final: 0.7424 (m) REVERT: A 408 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8359 (tttm) REVERT: B 102 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7978 (ttmm) REVERT: B 108 LYS cc_start: 0.7441 (mttt) cc_final: 0.7239 (ttmm) REVERT: B 138 ASP cc_start: 0.7711 (m-30) cc_final: 0.7325 (t0) REVERT: B 302 ASP cc_start: 0.8114 (m-30) cc_final: 0.7802 (m-30) REVERT: B 321 GLU cc_start: 0.6418 (mt-10) cc_final: 0.5680 (pt0) REVERT: B 331 LYS cc_start: 0.7541 (tttt) cc_final: 0.7059 (ttpp) REVERT: B 418 GLN cc_start: 0.6705 (tp40) cc_final: 0.6469 (pp30) REVERT: B 560 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6800 (mm-30) REVERT: B 655 TRP cc_start: 0.7901 (m100) cc_final: 0.7516 (t-100) REVERT: C 164 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7337 (mt0) REVERT: C 169 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8165 (mptt) REVERT: D 1 MET cc_start: 0.5329 (mtm) cc_final: 0.4553 (mtm) outliers start: 11 outliers final: 5 residues processed: 120 average time/residue: 1.0809 time to fit residues: 142.3714 Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089691 restraints weight = 37772.089| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.13 r_work: 0.2931 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11060 Z= 0.161 Angle : 0.526 5.906 15039 Z= 0.277 Chirality : 0.039 0.151 1807 Planarity : 0.004 0.046 1906 Dihedral : 7.007 74.644 1569 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.23 % Allowed : 12.33 % Favored : 86.43 % 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: 0.03 (0.22), residues: 1442 helix: 1.56 (0.18), residues: 853 sheet: -3.00 (0.44), residues: 106 loop : -2.14 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.024 0.001 TYR A 381 PHE 0.015 0.001 PHE A 109 TRP 0.006 0.001 TRP B 71 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00382 (11060) covalent geometry : angle 0.52550 (15039) hydrogen bonds : bond 0.04948 ( 661) hydrogen bonds : angle 4.39039 ( 1941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.5655 (ptt-90) REVERT: A 116 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7084 (ptm-80) REVERT: A 205 ASN cc_start: 0.7479 (p0) cc_final: 0.6975 (p0) REVERT: A 274 MET cc_start: 0.8292 (mmt) cc_final: 0.8030 (mmt) REVERT: A 408 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8083 (tttm) REVERT: B 102 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7817 (ttmm) REVERT: B 138 ASP cc_start: 0.7462 (m-30) cc_final: 0.7061 (t0) REVERT: B 302 ASP cc_start: 0.8007 (m-30) cc_final: 0.7604 (m-30) REVERT: B 321 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5291 (pt0) REVERT: B 331 LYS cc_start: 0.7450 (tttt) cc_final: 0.6979 (ttpp) REVERT: B 418 GLN cc_start: 0.6700 (tp40) cc_final: 0.6477 (pp30) REVERT: B 560 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6469 (mm-30) REVERT: B 655 TRP cc_start: 0.7662 (m100) cc_final: 0.7413 (t-100) REVERT: C 164 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7019 (mt0) REVERT: C 169 LYS cc_start: 0.8763 (ttmm) cc_final: 0.7995 (mptt) REVERT: D 1 MET cc_start: 0.5353 (mtm) cc_final: 0.4552 (mtm) outliers start: 14 outliers final: 7 residues processed: 117 average time/residue: 1.1059 time to fit residues: 142.2430 Evaluate side-chains 115 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 34 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.122247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.090175 restraints weight = 38159.292| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.15 r_work: 0.2939 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11060 Z= 0.146 Angle : 0.516 5.792 15039 Z= 0.271 Chirality : 0.038 0.147 1807 Planarity : 0.004 0.044 1906 Dihedral : 6.623 73.387 1569 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.06 % Allowed : 13.30 % Favored : 85.64 % 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: 0.17 (0.23), residues: 1442 helix: 1.64 (0.18), residues: 859 sheet: -2.93 (0.44), residues: 106 loop : -2.06 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.023 0.001 TYR A 381 PHE 0.015 0.001 PHE A 109 TRP 0.006 0.001 TRP A 59 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00343 (11060) covalent geometry : angle 0.51623 (15039) hydrogen bonds : bond 0.04746 ( 661) hydrogen bonds : angle 4.33029 ( 1941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU D 27 " (corrupted residue). Skipping it. REVERT: A 55 ARG cc_start: 0.7005 (ttp-110) cc_final: 0.5629 (ptt-90) REVERT: A 116 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7079 (ptm-80) REVERT: A 205 ASN cc_start: 0.7383 (p0) cc_final: 0.6939 (p0) REVERT: A 274 MET cc_start: 0.8277 (mmt) cc_final: 0.8045 (mmt) REVERT: A 378 SER cc_start: 0.7145 (t) cc_final: 0.6910 (m) REVERT: A 408 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8088 (tttm) REVERT: B 102 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7813 (ttmm) REVERT: B 138 ASP cc_start: 0.7459 (m-30) cc_final: 0.7074 (t0) REVERT: B 302 ASP cc_start: 0.8003 (m-30) cc_final: 0.7557 (m-30) REVERT: B 321 GLU cc_start: 0.5975 (mt-10) cc_final: 0.5252 (pt0) REVERT: B 331 LYS cc_start: 0.7443 (tttt) cc_final: 0.6972 (ttpp) REVERT: B 375 VAL cc_start: 0.7797 (t) cc_final: 0.7369 (p) REVERT: B 418 GLN cc_start: 0.6694 (tp40) cc_final: 0.6477 (pp30) REVERT: B 560 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6469 (mm-30) REVERT: B 655 TRP cc_start: 0.7756 (m100) cc_final: 0.7505 (t-100) REVERT: C 164 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7000 (mt0) REVERT: C 169 LYS cc_start: 0.8750 (ttmm) cc_final: 0.7984 (mptt) REVERT: D 1 MET cc_start: 0.5347 (mtm) cc_final: 0.4545 (mtm) outliers start: 12 outliers final: 5 residues processed: 121 average time/residue: 1.1043 time to fit residues: 146.4538 Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.121290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088997 restraints weight = 37836.143| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.19 r_work: 0.2921 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11060 Z= 0.171 Angle : 0.529 5.926 15039 Z= 0.279 Chirality : 0.039 0.151 1807 Planarity : 0.004 0.044 1906 Dihedral : 6.519 74.316 1569 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.06 % Allowed : 13.48 % Favored : 85.46 % 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: 0.18 (0.22), residues: 1442 helix: 1.64 (0.18), residues: 860 sheet: -2.88 (0.45), residues: 106 loop : -2.06 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 110 TYR 0.023 0.002 TYR A 381 PHE 0.015 0.001 PHE A 109 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00411 (11060) covalent geometry : angle 0.52917 (15039) hydrogen bonds : bond 0.04982 ( 661) hydrogen bonds : angle 4.35891 ( 1941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU D 27 " (corrupted residue). Skipping it. REVERT: A 55 ARG cc_start: 0.7223 (ttp-110) cc_final: 0.5866 (ptt-90) REVERT: A 116 ARG cc_start: 0.8036 (mtm110) cc_final: 0.7249 (ptm-80) REVERT: A 205 ASN cc_start: 0.7565 (p0) cc_final: 0.7130 (p0) REVERT: A 274 MET cc_start: 0.8443 (mmt) cc_final: 0.8222 (mmt) REVERT: A 408 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8247 (tttm) REVERT: B 102 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8065 (ttmm) REVERT: B 138 ASP cc_start: 0.7685 (m-30) cc_final: 0.7287 (t0) REVERT: B 302 ASP cc_start: 0.8108 (m-30) cc_final: 0.7757 (m-30) REVERT: B 321 GLU cc_start: 0.6357 (mt-10) cc_final: 0.5699 (pt0) REVERT: B 331 LYS cc_start: 0.7529 (tttt) cc_final: 0.7042 (ttpp) REVERT: B 375 VAL cc_start: 0.7932 (t) cc_final: 0.7505 (p) REVERT: B 383 MET cc_start: 0.8187 (ptt) cc_final: 0.7936 (ptt) REVERT: B 418 GLN cc_start: 0.6714 (tp40) cc_final: 0.6488 (pp30) REVERT: B 515 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7687 (ttt) REVERT: B 560 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: C 164 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7220 (mt0) REVERT: C 169 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8150 (mptt) REVERT: D 1 MET cc_start: 0.5386 (mtm) cc_final: 0.4592 (mtm) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 1.0429 time to fit residues: 133.0084 Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 96 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.123556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091424 restraints weight = 37490.419| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.14 r_work: 0.2958 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11060 Z= 0.111 Angle : 0.494 5.622 15039 Z= 0.258 Chirality : 0.038 0.142 1807 Planarity : 0.004 0.042 1906 Dihedral : 6.268 71.683 1569 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.79 % Allowed : 13.92 % Favored : 85.29 % 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: 0.42 (0.23), residues: 1442 helix: 1.81 (0.18), residues: 862 sheet: -2.79 (0.45), residues: 106 loop : -1.93 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 110 TYR 0.023 0.001 TYR A 381 PHE 0.013 0.001 PHE A 109 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00249 (11060) covalent geometry : angle 0.49400 (15039) hydrogen bonds : bond 0.04322 ( 661) hydrogen bonds : angle 4.22423 ( 1941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU D 27 " (corrupted residue). Skipping it. REVERT: A 55 ARG cc_start: 0.6998 (ttp-110) cc_final: 0.5625 (ptt-90) REVERT: A 116 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7054 (ptm-80) REVERT: A 205 ASN cc_start: 0.7343 (p0) cc_final: 0.6877 (p0) REVERT: A 274 MET cc_start: 0.8283 (mmt) cc_final: 0.8067 (mmt) REVERT: A 378 SER cc_start: 0.7030 (t) cc_final: 0.6806 (m) REVERT: A 408 LYS cc_start: 0.8375 (ttpt) cc_final: 0.8081 (tttm) REVERT: B 102 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7973 (ttmm) REVERT: B 138 ASP cc_start: 0.7419 (m-30) cc_final: 0.7051 (t0) REVERT: B 302 ASP cc_start: 0.7987 (m-30) cc_final: 0.7543 (m-30) REVERT: B 321 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5316 (pt0) REVERT: B 331 LYS cc_start: 0.7400 (tttt) cc_final: 0.6622 (tppt) REVERT: B 375 VAL cc_start: 0.7783 (t) cc_final: 0.7364 (p) REVERT: B 383 MET cc_start: 0.8013 (ptt) cc_final: 0.7754 (ptt) REVERT: B 418 GLN cc_start: 0.6772 (tp40) cc_final: 0.6555 (pp30) REVERT: B 515 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7452 (ttt) REVERT: B 560 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6491 (mm-30) REVERT: C 164 GLN cc_start: 0.8219 (tp-100) cc_final: 0.6804 (mt0) REVERT: C 169 LYS cc_start: 0.8732 (ttmm) cc_final: 0.7990 (mppt) REVERT: D 1 MET cc_start: 0.5333 (mtm) cc_final: 0.4526 (mtm) outliers start: 9 outliers final: 3 residues processed: 115 average time/residue: 1.0414 time to fit residues: 132.0207 Evaluate side-chains 114 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 617 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.122583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090447 restraints weight = 37917.821| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.15 r_work: 0.2943 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11060 Z= 0.142 Angle : 0.509 5.802 15039 Z= 0.266 Chirality : 0.038 0.144 1807 Planarity : 0.004 0.042 1906 Dihedral : 6.287 73.171 1569 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.62 % Allowed : 14.19 % Favored : 85.20 % 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: 0.45 (0.23), residues: 1442 helix: 1.84 (0.18), residues: 861 sheet: -2.76 (0.45), residues: 106 loop : -1.93 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 110 TYR 0.023 0.001 TYR A 381 PHE 0.013 0.001 PHE A 109 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00337 (11060) covalent geometry : angle 0.50863 (15039) hydrogen bonds : bond 0.04582 ( 661) hydrogen bonds : angle 4.24844 ( 1941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU D 27 " (corrupted residue). Skipping it. REVERT: A 55 ARG cc_start: 0.6997 (ttp-110) cc_final: 0.5626 (ptt-90) REVERT: A 116 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7082 (ptm-80) REVERT: A 205 ASN cc_start: 0.7319 (p0) cc_final: 0.6864 (p0) REVERT: A 274 MET cc_start: 0.8303 (mmt) cc_final: 0.8029 (mmt) REVERT: A 408 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8086 (tttm) REVERT: B 102 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7975 (ttmm) REVERT: B 138 ASP cc_start: 0.7447 (m-30) cc_final: 0.7067 (t0) REVERT: B 302 ASP cc_start: 0.8004 (m-30) cc_final: 0.7560 (m-30) REVERT: B 321 GLU cc_start: 0.5993 (mt-10) cc_final: 0.5375 (pt0) REVERT: B 331 LYS cc_start: 0.7408 (tttt) cc_final: 0.6627 (tppt) REVERT: B 375 VAL cc_start: 0.7781 (t) cc_final: 0.7361 (p) REVERT: B 383 MET cc_start: 0.8028 (ptt) cc_final: 0.7754 (ptt) REVERT: B 418 GLN cc_start: 0.6819 (tp40) cc_final: 0.6593 (pp30) REVERT: B 515 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7488 (ttt) REVERT: B 560 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6537 (mm-30) REVERT: C 164 GLN cc_start: 0.8228 (tp-100) cc_final: 0.6830 (mt0) REVERT: C 169 LYS cc_start: 0.8725 (ttmm) cc_final: 0.7989 (mptt) REVERT: D 1 MET cc_start: 0.5363 (mtm) cc_final: 0.4565 (mtm) outliers start: 7 outliers final: 5 residues processed: 114 average time/residue: 1.0542 time to fit residues: 132.6554 Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.124273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091300 restraints weight = 37773.822| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.18 r_work: 0.2942 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11060 Z= 0.138 Angle : 0.508 5.745 15039 Z= 0.266 Chirality : 0.038 0.144 1807 Planarity : 0.004 0.041 1906 Dihedral : 6.260 73.394 1569 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.70 % Allowed : 14.27 % Favored : 85.02 % 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: 0.49 (0.23), residues: 1442 helix: 1.87 (0.18), residues: 862 sheet: -2.67 (0.46), residues: 106 loop : -1.92 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 110 TYR 0.023 0.001 TYR A 381 PHE 0.014 0.001 PHE A 109 TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00325 (11060) covalent geometry : angle 0.50808 (15039) hydrogen bonds : bond 0.04568 ( 661) hydrogen bonds : angle 4.23752 ( 1941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU D 27 " (corrupted residue). Skipping it. REVERT: A 55 ARG cc_start: 0.7079 (ttp-110) cc_final: 0.5719 (ptt-90) REVERT: A 116 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7177 (ptm-80) REVERT: A 205 ASN cc_start: 0.7394 (p0) cc_final: 0.6949 (p0) REVERT: A 274 MET cc_start: 0.8375 (mmt) cc_final: 0.8112 (mmt) REVERT: A 378 SER cc_start: 0.7321 (t) cc_final: 0.7067 (m) REVERT: A 408 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8158 (tttm) REVERT: B 102 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8029 (ttmm) REVERT: B 138 ASP cc_start: 0.7524 (m-30) cc_final: 0.7140 (t0) REVERT: B 302 ASP cc_start: 0.8048 (m-30) cc_final: 0.7676 (m-30) REVERT: B 321 GLU cc_start: 0.6130 (mt-10) cc_final: 0.5497 (pt0) REVERT: B 331 LYS cc_start: 0.7438 (tttt) cc_final: 0.6651 (tppt) REVERT: B 375 VAL cc_start: 0.7818 (t) cc_final: 0.7400 (p) REVERT: B 383 MET cc_start: 0.8068 (ptt) cc_final: 0.7791 (ptt) REVERT: B 418 GLN cc_start: 0.6821 (tp40) cc_final: 0.6594 (pp30) REVERT: B 515 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7498 (ttt) REVERT: B 560 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: C 164 GLN cc_start: 0.8305 (tp-100) cc_final: 0.6939 (mt0) REVERT: C 169 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8047 (mptt) REVERT: D 1 MET cc_start: 0.5375 (mtm) cc_final: 0.4580 (mtm) outliers start: 8 outliers final: 5 residues processed: 118 average time/residue: 1.0688 time to fit residues: 138.9031 Evaluate side-chains 120 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 63 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 122 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.123225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091160 restraints weight = 37632.624| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.14 r_work: 0.2955 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11060 Z= 0.124 Angle : 0.498 5.671 15039 Z= 0.260 Chirality : 0.038 0.142 1807 Planarity : 0.004 0.041 1906 Dihedral : 6.183 72.868 1569 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.79 % Allowed : 14.10 % Favored : 85.11 % 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: 0.57 (0.23), residues: 1442 helix: 1.93 (0.18), residues: 863 sheet: -2.62 (0.46), residues: 106 loop : -1.90 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 110 TYR 0.023 0.001 TYR A 381 PHE 0.013 0.001 PHE A 109 TRP 0.008 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00285 (11060) covalent geometry : angle 0.49793 (15039) hydrogen bonds : bond 0.04382 ( 661) hydrogen bonds : angle 4.19561 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6177.02 seconds wall clock time: 105 minutes 0.21 seconds (6300.21 seconds total)