Starting phenix.real_space_refine on Thu Jul 2 19:09:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i04_52550/07_2026/9i04_52550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i04_52550/07_2026/9i04_52550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i04_52550/07_2026/9i04_52550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i04_52550/07_2026/9i04_52550.map" model { file = "/net/cci-nas-00/data/ceres_data/9i04_52550/07_2026/9i04_52550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i04_52550/07_2026/9i04_52550.cif" } resolution = 4.05 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= 0.027 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 P 28 5.49 5 S 45 5.16 5 C 5936 2.51 5 N 1620 2.21 5 O 1840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 9469 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3957 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 467} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4232 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 506} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 703 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 85} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 292 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Time building chain proxies: 2.02, per 1000 atoms: 0.21 Number of scatterers: 9469 At special positions: 0 Unit cell: (84.5973, 115.674, 132.939, 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) S 45 16.00 P 28 15.00 O 1840 8.00 N 1620 7.00 C 5936 6.00 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: 0.93 Conformation dependent library (CDL) restraints added in 333.7 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 37.8% alpha, 19.6% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.697A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.851A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 470 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 519 through 527 removed outlier: 4.351A pdb=" N ASP A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.680A pdb=" N SER B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.620A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.582A pdb=" N THR B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 233 No H-bonds generated for 'chain 'B' and resid 232 through 233' Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.645A pdb=" N LYS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.871A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.606A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 535 removed outlier: 3.699A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix removed outlier: 3.579A pdb=" N THR B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 53 Processing helix chain 'C' and resid 75 through 89 Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.652A pdb=" N LEU C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 5.071A pdb=" N VAL A 104 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 87 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 108 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU A 83 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 38 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR A 88 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 42 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 43 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.666A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 395 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A 350 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 304 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 84 removed outlier: 5.373A pdb=" N VAL B 79 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B 58 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 83 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE B 54 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 247 through 253 removed outlier: 6.804A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU B 268 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N ASN B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.266A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AA9, first strand: chain 'B' and resid 464 through 467 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.094A pdb=" N ILE C 32 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 70 " --> pdb=" O TYR C 33 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2604 1.33 - 1.45: 1612 1.45 - 1.57: 5370 1.57 - 1.69: 54 1.69 - 1.81: 74 Bond restraints: 9714 Sorted by residual: bond pdb=" C3' DT E 7 " pdb=" C2' DT E 7 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DG E 8 " pdb=" C2' DG E 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 bond pdb=" C1' DT E 7 " pdb=" N1 DT E 7 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.85e+00 bond pdb=" C3' DC E 4 " pdb=" O3' DC E 4 " ideal model delta sigma weight residual 1.435 1.407 0.028 1.30e-02 5.92e+03 4.50e+00 bond pdb=" C3' DA E 13 " pdb=" C2' DA E 13 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.17e+00 ... (remaining 9709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 12846 1.51 - 3.02: 330 3.02 - 4.53: 44 4.53 - 6.04: 11 6.04 - 7.55: 2 Bond angle restraints: 13233 Sorted by residual: angle pdb=" N3 DT D 3 " pdb=" C4 DT D 3 " pdb=" O4 DT D 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT E 10 " pdb=" C4 DT E 10 " pdb=" O4 DT E 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT E 7 " pdb=" C4 DT E 7 " pdb=" O4 DT E 7 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" O4' DA D 11 " pdb=" C4' DA D 11 " pdb=" C3' DA D 11 " ideal model delta sigma weight residual 106.00 103.65 2.35 6.00e-01 2.78e+00 1.53e+01 ... (remaining 13228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.13: 5556 30.13 - 60.27: 297 60.27 - 90.40: 32 90.40 - 120.53: 1 120.53 - 150.66: 1 Dihedral angle restraints: 5887 sinusoidal: 2620 harmonic: 3267 Sorted by residual: dihedral pdb=" C4' DT E 10 " pdb=" C3' DT E 10 " pdb=" O3' DT E 10 " pdb=" P DG E 11 " ideal model delta sinusoidal sigma weight residual -140.00 10.66 -150.66 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA ASP B 177 " pdb=" CB ASP B 177 " pdb=" CG ASP B 177 " pdb=" OD1 ASP B 177 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA SER B 318 " pdb=" C SER B 318 " pdb=" N ASP B 319 " pdb=" CA ASP B 319 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 955 0.033 - 0.065: 357 0.065 - 0.098: 112 0.098 - 0.130: 56 0.130 - 0.163: 3 Chirality restraints: 1483 Sorted by residual: chirality pdb=" CA GLU C 36 " pdb=" N GLU C 36 " pdb=" C GLU C 36 " pdb=" CB GLU C 36 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" P DG E 11 " pdb=" OP1 DG E 11 " pdb=" OP2 DG E 11 " pdb=" O5' DG E 11 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1480 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT E 7 " -0.022 2.00e-02 2.50e+03 1.05e-02 2.77e+00 pdb=" N1 DT E 7 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT E 7 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT E 7 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT E 7 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT E 7 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT E 7 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT E 7 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT E 7 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT E 7 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 115 " 0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO C 116 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 216 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C GLU B 216 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU B 216 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY B 217 " -0.009 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4235 2.94 - 3.43: 10666 3.43 - 3.92: 16981 3.92 - 4.41: 19190 4.41 - 4.90: 28855 Nonbonded interactions: 79927 Sorted by model distance: nonbonded pdb=" O ASP A 523 " pdb=" OE1 GLU A 527 " model vdw 2.451 3.040 nonbonded pdb=" O LYS A 331 " pdb=" OE1 GLU A 335 " model vdw 2.531 3.040 nonbonded pdb=" O5' DG E 6 " pdb=" O4' DG E 6 " model vdw 2.533 2.432 nonbonded pdb=" O LYS A 331 " pdb=" OG1 THR A 334 " model vdw 2.564 3.040 nonbonded pdb=" N1 DG E 11 " pdb=" C4 DG E 11 " model vdw 2.595 2.672 ... (remaining 79922 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 group one per residue 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: 0.530 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 0.039 9714 Z= 0.208 Angle : 0.576 7.548 13233 Z= 0.366 Chirality : 0.041 0.163 1483 Planarity : 0.004 0.042 1615 Dihedral : 17.414 150.663 3761 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.25 (0.26), residues: 1112 helix: 1.25 (0.26), residues: 386 sheet: -0.97 (0.36), residues: 185 loop : -0.10 (0.29), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 325 TYR 0.007 0.001 TYR B 333 PHE 0.009 0.001 PHE B 323 TRP 0.007 0.001 TRP C 82 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.21 ( 9714) covalent geometry : angle 0.57567 / 0.37 (13233) hydrogen bonds : bond 0.11601 / 7.42 ( 390) hydrogen bonds : angle 6.31110 / 4.54 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.9480 (mpp) cc_final: 0.9265 (mpp) REVERT: A 135 MET cc_start: 0.8522 (mpp) cc_final: 0.8320 (mpp) REVERT: A 167 MET cc_start: 0.9107 (tpp) cc_final: 0.8488 (tpp) REVERT: A 168 LEU cc_start: 0.9851 (tp) cc_final: 0.9124 (tp) REVERT: A 203 MET cc_start: 0.8907 (mpp) cc_final: 0.7437 (mpp) REVERT: A 279 LYS cc_start: 0.9411 (mmtt) cc_final: 0.8495 (mmtt) REVERT: A 346 MET cc_start: 0.8683 (tpt) cc_final: 0.8384 (tpp) REVERT: A 348 MET cc_start: 0.9467 (mmp) cc_final: 0.8547 (mmm) REVERT: A 514 MET cc_start: 0.9090 (ptt) cc_final: 0.8550 (ptt) REVERT: B 20 MET cc_start: 0.7293 (mmp) cc_final: 0.7039 (mmm) REVERT: B 84 MET cc_start: 0.9498 (pmm) cc_final: 0.9164 (pmm) REVERT: B 212 MET cc_start: 0.9643 (mmp) cc_final: 0.9425 (mmm) REVERT: B 389 MET cc_start: 0.8098 (tpp) cc_final: 0.7450 (tpp) REVERT: B 461 MET cc_start: 0.9086 (ttt) cc_final: 0.8425 (ttt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0832 time to fit residues: 7.9529 Evaluate side-chains 51 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 overall best weight: 2.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028699 restraints weight = 85707.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029629 restraints weight = 52033.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.030255 restraints weight = 37410.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.030701 restraints weight = 29949.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.030990 restraints weight = 25636.162| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9714 Z= 0.169 Angle : 0.556 8.362 13233 Z= 0.296 Chirality : 0.042 0.211 1483 Planarity : 0.004 0.037 1615 Dihedral : 17.475 150.227 1495 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % 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: 0.35 (0.26), residues: 1112 helix: 1.35 (0.26), residues: 389 sheet: -0.97 (0.36), residues: 180 loop : -0.05 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 325 TYR 0.011 0.001 TYR B 397 PHE 0.010 0.001 PHE B 59 TRP 0.005 0.001 TRP C 82 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 ( 9714) covalent geometry : angle 0.55585 / 0.30 (13233) hydrogen bonds : bond 0.03630 / 2.35 ( 390) hydrogen bonds : angle 5.52935 / 3.98 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9383 (mpp) cc_final: 0.9121 (mpp) REVERT: A 87 PHE cc_start: 0.9426 (m-10) cc_final: 0.8692 (m-80) REVERT: A 168 LEU cc_start: 0.9841 (tp) cc_final: 0.9585 (tp) REVERT: A 203 MET cc_start: 0.8704 (mpp) cc_final: 0.8319 (mpp) REVERT: A 279 LYS cc_start: 0.9347 (mmtt) cc_final: 0.8488 (mmtt) REVERT: A 346 MET cc_start: 0.8832 (tpt) cc_final: 0.8553 (tpp) REVERT: A 348 MET cc_start: 0.9441 (mmp) cc_final: 0.8580 (mmm) REVERT: A 496 ASP cc_start: 0.9208 (t0) cc_final: 0.9007 (t0) REVERT: B 212 MET cc_start: 0.9632 (mmp) cc_final: 0.9415 (mmm) REVERT: B 389 MET cc_start: 0.8394 (tpp) cc_final: 0.8193 (tpp) REVERT: B 461 MET cc_start: 0.8954 (ttt) cc_final: 0.8191 (ttt) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0774 time to fit residues: 7.2314 Evaluate side-chains 49 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.037109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.028361 restraints weight = 86446.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029299 restraints weight = 51796.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.029937 restraints weight = 37003.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.030358 restraints weight = 29479.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030658 restraints weight = 25362.702| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9714 Z= 0.207 Angle : 0.584 7.707 13233 Z= 0.309 Chirality : 0.042 0.196 1483 Planarity : 0.004 0.036 1615 Dihedral : 17.551 153.381 1495 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.31 (0.26), residues: 1112 helix: 1.30 (0.26), residues: 393 sheet: -1.01 (0.36), residues: 179 loop : -0.06 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.011 0.001 TYR B 333 PHE 0.010 0.001 PHE A 131 TRP 0.005 0.001 TRP C 82 HIS 0.004 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 ( 9714) covalent geometry : angle 0.58393 / 0.31 (13233) hydrogen bonds : bond 0.03549 / 2.31 ( 390) hydrogen bonds : angle 5.41313 / 3.94 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9344 (mpp) cc_final: 0.9052 (mpp) REVERT: A 168 LEU cc_start: 0.9844 (tp) cc_final: 0.9579 (tp) REVERT: A 203 MET cc_start: 0.8702 (mpp) cc_final: 0.8289 (mpp) REVERT: A 279 LYS cc_start: 0.9397 (mmtt) cc_final: 0.8571 (mmtt) REVERT: A 348 MET cc_start: 0.9311 (mmp) cc_final: 0.8460 (mmm) REVERT: A 496 ASP cc_start: 0.9247 (t0) cc_final: 0.9038 (t0) REVERT: B 461 MET cc_start: 0.8932 (ttt) cc_final: 0.8291 (ttt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0746 time to fit residues: 7.2335 Evaluate side-chains 50 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN B 432 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.029097 restraints weight = 83788.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.030076 restraints weight = 50194.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.030753 restraints weight = 35660.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031222 restraints weight = 28231.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.031531 restraints weight = 23978.365| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9714 Z= 0.111 Angle : 0.530 7.657 13233 Z= 0.281 Chirality : 0.042 0.186 1483 Planarity : 0.003 0.035 1615 Dihedral : 17.521 151.613 1495 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 1112 helix: 1.52 (0.27), residues: 389 sheet: -0.87 (0.36), residues: 184 loop : -0.02 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.009 0.001 TYR B 333 PHE 0.008 0.001 PHE A 350 TRP 0.005 0.001 TRP C 82 HIS 0.002 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 9714) covalent geometry : angle 0.53049 / 0.28 (13233) hydrogen bonds : bond 0.03137 / 2.04 ( 390) hydrogen bonds : angle 5.14924 / 3.73 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9221 (t70) cc_final: 0.8818 (t70) REVERT: A 62 MET cc_start: 0.9362 (mpp) cc_final: 0.9029 (mmm) REVERT: A 87 PHE cc_start: 0.9187 (m-80) cc_final: 0.8497 (m-80) REVERT: A 135 MET cc_start: 0.9255 (mpp) cc_final: 0.8886 (mpp) REVERT: A 168 LEU cc_start: 0.9837 (tp) cc_final: 0.9577 (tp) REVERT: A 279 LYS cc_start: 0.9338 (mmtt) cc_final: 0.8540 (mmtt) REVERT: A 348 MET cc_start: 0.9256 (mmp) cc_final: 0.8631 (mmm) REVERT: A 434 LEU cc_start: 0.9343 (tp) cc_final: 0.9140 (tp) REVERT: A 496 ASP cc_start: 0.9221 (t0) cc_final: 0.8994 (t0) REVERT: A 514 MET cc_start: 0.9104 (ptt) cc_final: 0.8501 (ppp) REVERT: B 84 MET cc_start: 0.9505 (pmm) cc_final: 0.9127 (pmm) REVERT: B 212 MET cc_start: 0.9563 (mmp) cc_final: 0.9296 (mmm) REVERT: B 461 MET cc_start: 0.8823 (ttt) cc_final: 0.8149 (ttt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0725 time to fit residues: 7.0312 Evaluate side-chains 51 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 0.0270 chunk 15 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.038303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029370 restraints weight = 85963.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.030341 restraints weight = 51519.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031010 restraints weight = 36684.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.031449 restraints weight = 29109.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.031689 restraints weight = 24941.896| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9714 Z= 0.122 Angle : 0.520 7.497 13233 Z= 0.276 Chirality : 0.041 0.188 1483 Planarity : 0.003 0.036 1615 Dihedral : 17.520 151.013 1495 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.54 (0.26), residues: 1112 helix: 1.57 (0.27), residues: 389 sheet: -0.86 (0.36), residues: 175 loop : 0.00 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.011 0.001 TYR B 333 PHE 0.008 0.001 PHE B 59 TRP 0.005 0.001 TRP C 82 HIS 0.002 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 9714) covalent geometry : angle 0.52005 / 0.28 (13233) hydrogen bonds : bond 0.03070 / 2.02 ( 390) hydrogen bonds : angle 5.05380 / 3.66 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9290 (t70) cc_final: 0.8844 (t0) REVERT: A 62 MET cc_start: 0.9384 (mpp) cc_final: 0.9151 (mpp) REVERT: A 87 PHE cc_start: 0.9192 (m-80) cc_final: 0.8522 (m-80) REVERT: A 135 MET cc_start: 0.9206 (mpp) cc_final: 0.8884 (mpp) REVERT: A 168 LEU cc_start: 0.9842 (tp) cc_final: 0.9585 (tp) REVERT: A 279 LYS cc_start: 0.9342 (mmtt) cc_final: 0.8676 (mmtm) REVERT: A 348 MET cc_start: 0.9206 (mmp) cc_final: 0.8542 (mmm) REVERT: A 434 LEU cc_start: 0.9353 (tp) cc_final: 0.9148 (tp) REVERT: A 496 ASP cc_start: 0.9249 (t0) cc_final: 0.9023 (t0) REVERT: B 14 MET cc_start: 0.9102 (tpt) cc_final: 0.8760 (mmm) REVERT: B 212 MET cc_start: 0.9634 (mmp) cc_final: 0.9389 (mmm) REVERT: B 389 MET cc_start: 0.8209 (tpp) cc_final: 0.7510 (tpp) REVERT: B 461 MET cc_start: 0.8810 (ttt) cc_final: 0.8124 (ttt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0827 time to fit residues: 8.2211 Evaluate side-chains 53 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.028926 restraints weight = 84759.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029870 restraints weight = 51178.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030509 restraints weight = 36697.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030968 restraints weight = 29299.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.031272 restraints weight = 24980.005| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9714 Z= 0.138 Angle : 0.527 7.405 13233 Z= 0.279 Chirality : 0.041 0.185 1483 Planarity : 0.003 0.039 1615 Dihedral : 17.558 151.306 1495 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 0.53 (0.26), residues: 1112 helix: 1.59 (0.26), residues: 393 sheet: -0.91 (0.35), residues: 184 loop : -0.01 (0.30), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.010 0.001 TYR B 333 PHE 0.008 0.001 PHE B 59 TRP 0.005 0.001 TRP C 82 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 9714) covalent geometry : angle 0.52743 / 0.28 (13233) hydrogen bonds : bond 0.03044 / 2.01 ( 390) hydrogen bonds : angle 5.00853 / 3.63 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9286 (t70) cc_final: 0.9035 (t70) REVERT: A 62 MET cc_start: 0.9351 (mpp) cc_final: 0.9089 (mpp) REVERT: A 87 PHE cc_start: 0.9264 (m-80) cc_final: 0.8697 (m-80) REVERT: A 135 MET cc_start: 0.9207 (mpp) cc_final: 0.8880 (mpp) REVERT: A 168 LEU cc_start: 0.9841 (tp) cc_final: 0.9625 (tp) REVERT: A 279 LYS cc_start: 0.9387 (mmtt) cc_final: 0.8568 (mmtt) REVERT: A 348 MET cc_start: 0.9136 (mmp) cc_final: 0.8528 (mmm) REVERT: A 434 LEU cc_start: 0.9379 (tp) cc_final: 0.9177 (tp) REVERT: A 496 ASP cc_start: 0.9237 (t0) cc_final: 0.9009 (t0) REVERT: A 514 MET cc_start: 0.9131 (ptt) cc_final: 0.8529 (ppp) REVERT: B 14 MET cc_start: 0.9083 (tpt) cc_final: 0.8819 (mmm) REVERT: B 84 MET cc_start: 0.9518 (pmm) cc_final: 0.9254 (pmm) REVERT: B 212 MET cc_start: 0.9539 (mmp) cc_final: 0.9307 (mmm) REVERT: B 389 MET cc_start: 0.8317 (tpp) cc_final: 0.7791 (mmm) REVERT: B 461 MET cc_start: 0.8842 (ttt) cc_final: 0.8131 (ttt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0859 time to fit residues: 7.9867 Evaluate side-chains 52 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN B 432 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028614 restraints weight = 85185.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029552 restraints weight = 51562.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030201 restraints weight = 37009.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.030653 restraints weight = 29399.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030879 restraints weight = 25081.261| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9714 Z= 0.165 Angle : 0.550 7.442 13233 Z= 0.290 Chirality : 0.041 0.187 1483 Planarity : 0.004 0.039 1615 Dihedral : 17.571 152.235 1495 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.47 (0.26), residues: 1112 helix: 1.53 (0.27), residues: 393 sheet: -0.96 (0.35), residues: 185 loop : -0.02 (0.30), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 489 TYR 0.011 0.001 TYR B 333 PHE 0.009 0.001 PHE A 525 TRP 0.006 0.001 TRP C 82 HIS 0.004 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 ( 9714) covalent geometry : angle 0.54980 / 0.29 (13233) hydrogen bonds : bond 0.03080 / 2.02 ( 390) hydrogen bonds : angle 5.10093 / 3.69 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9274 (t70) cc_final: 0.8850 (t70) REVERT: A 62 MET cc_start: 0.9349 (mpp) cc_final: 0.9059 (mmm) REVERT: A 87 PHE cc_start: 0.9289 (m-80) cc_final: 0.8722 (m-80) REVERT: A 168 LEU cc_start: 0.9840 (tp) cc_final: 0.9629 (tp) REVERT: A 279 LYS cc_start: 0.9360 (mmtt) cc_final: 0.8575 (mmtt) REVERT: A 348 MET cc_start: 0.9207 (mmp) cc_final: 0.8522 (mmm) REVERT: A 496 ASP cc_start: 0.9249 (t0) cc_final: 0.9028 (t0) REVERT: B 212 MET cc_start: 0.9614 (mmp) cc_final: 0.9410 (mmm) REVERT: B 389 MET cc_start: 0.8386 (tpp) cc_final: 0.8152 (tpp) REVERT: B 461 MET cc_start: 0.8850 (ttt) cc_final: 0.8136 (ttt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0887 time to fit residues: 8.5901 Evaluate side-chains 53 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.038571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029737 restraints weight = 84283.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030676 restraints weight = 50865.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031345 restraints weight = 36372.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.031809 restraints weight = 28859.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032122 restraints weight = 24615.371| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9714 Z= 0.102 Angle : 0.532 7.693 13233 Z= 0.278 Chirality : 0.042 0.179 1483 Planarity : 0.003 0.040 1615 Dihedral : 17.538 149.830 1495 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 0.63 (0.26), residues: 1112 helix: 1.63 (0.27), residues: 390 sheet: -0.80 (0.35), residues: 182 loop : 0.07 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.009 0.001 TYR A 400 PHE 0.008 0.001 PHE B 365 TRP 0.005 0.001 TRP C 82 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9714) covalent geometry : angle 0.53196 / 0.28 (13233) hydrogen bonds : bond 0.02881 / 1.89 ( 390) hydrogen bonds : angle 4.90415 / 3.54 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9268 (t70) cc_final: 0.8848 (t70) REVERT: A 62 MET cc_start: 0.9348 (mpp) cc_final: 0.9127 (mmm) REVERT: A 87 PHE cc_start: 0.9245 (m-80) cc_final: 0.8680 (m-80) REVERT: A 135 MET cc_start: 0.9256 (mpp) cc_final: 0.8917 (mpp) REVERT: A 167 MET cc_start: 0.9145 (tpp) cc_final: 0.8560 (mmm) REVERT: A 168 LEU cc_start: 0.9820 (tp) cc_final: 0.9459 (tp) REVERT: A 203 MET cc_start: 0.8589 (mpp) cc_final: 0.7759 (mpp) REVERT: A 279 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8400 (mmtt) REVERT: A 348 MET cc_start: 0.9168 (mmp) cc_final: 0.8536 (mmm) REVERT: A 434 LEU cc_start: 0.9326 (tp) cc_final: 0.9099 (tp) REVERT: A 496 ASP cc_start: 0.9201 (t0) cc_final: 0.8973 (t0) REVERT: A 514 MET cc_start: 0.9069 (ptt) cc_final: 0.8491 (ppp) REVERT: B 43 GLN cc_start: 0.9345 (mt0) cc_final: 0.9056 (tt0) REVERT: B 389 MET cc_start: 0.8356 (tpp) cc_final: 0.8110 (tpp) REVERT: B 461 MET cc_start: 0.8781 (ttt) cc_final: 0.8049 (ttt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0869 time to fit residues: 8.5233 Evaluate side-chains 52 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 108 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.038353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029396 restraints weight = 82715.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030357 restraints weight = 49988.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.031026 restraints weight = 35774.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031495 restraints weight = 28364.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.031805 restraints weight = 24099.822| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9714 Z= 0.101 Angle : 0.530 8.909 13233 Z= 0.276 Chirality : 0.042 0.180 1483 Planarity : 0.003 0.040 1615 Dihedral : 17.526 148.766 1495 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1112 helix: 1.72 (0.27), residues: 384 sheet: -0.72 (0.36), residues: 182 loop : 0.05 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.009 0.001 TYR B 333 PHE 0.010 0.001 PHE B 365 TRP 0.005 0.001 TRP C 82 HIS 0.002 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9714) covalent geometry : angle 0.53025 / 0.28 (13233) hydrogen bonds : bond 0.02871 / 1.89 ( 390) hydrogen bonds : angle 4.87196 / 3.52 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9252 (t70) cc_final: 0.8828 (t70) REVERT: A 62 MET cc_start: 0.9335 (mpp) cc_final: 0.9123 (mmm) REVERT: A 87 PHE cc_start: 0.9197 (m-80) cc_final: 0.8644 (m-80) REVERT: A 135 MET cc_start: 0.9237 (mpp) cc_final: 0.8948 (mpp) REVERT: A 167 MET cc_start: 0.9140 (tpp) cc_final: 0.8578 (mmm) REVERT: A 168 LEU cc_start: 0.9804 (tp) cc_final: 0.9547 (tp) REVERT: A 203 MET cc_start: 0.8469 (mpp) cc_final: 0.7868 (mpp) REVERT: A 279 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8446 (mmtt) REVERT: A 348 MET cc_start: 0.9148 (mmp) cc_final: 0.8525 (mmm) REVERT: A 434 LEU cc_start: 0.9326 (tp) cc_final: 0.9095 (tp) REVERT: A 496 ASP cc_start: 0.9193 (t0) cc_final: 0.8962 (t0) REVERT: A 514 MET cc_start: 0.9113 (ptt) cc_final: 0.8571 (ppp) REVERT: B 14 MET cc_start: 0.9198 (tpt) cc_final: 0.8871 (mmm) REVERT: B 84 MET cc_start: 0.9402 (pmm) cc_final: 0.8962 (pmm) REVERT: B 212 MET cc_start: 0.9699 (mmp) cc_final: 0.9483 (mmm) REVERT: B 389 MET cc_start: 0.8396 (tpp) cc_final: 0.8137 (tpp) REVERT: B 461 MET cc_start: 0.8765 (ttt) cc_final: 0.8026 (ttt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0853 time to fit residues: 8.2953 Evaluate side-chains 53 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 104 optimal weight: 0.2980 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 92 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.039072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030044 restraints weight = 81631.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.031010 restraints weight = 49240.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031682 restraints weight = 35260.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.032151 restraints weight = 27997.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.032464 restraints weight = 23845.332| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9714 Z= 0.094 Angle : 0.518 7.828 13233 Z= 0.268 Chirality : 0.041 0.174 1483 Planarity : 0.003 0.040 1615 Dihedral : 17.487 147.178 1495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.77 (0.27), residues: 1112 helix: 1.81 (0.27), residues: 384 sheet: -0.66 (0.36), residues: 182 loop : 0.09 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 232 TYR 0.009 0.001 TYR A 400 PHE 0.009 0.001 PHE B 59 TRP 0.006 0.001 TRP C 82 HIS 0.002 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 ( 9714) covalent geometry : angle 0.51752 / 0.27 (13233) hydrogen bonds : bond 0.02785 / 1.81 ( 390) hydrogen bonds : angle 4.77620 / 3.44 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9252 (t70) cc_final: 0.8870 (t70) REVERT: A 62 MET cc_start: 0.9334 (mpp) cc_final: 0.9083 (mmm) REVERT: A 87 PHE cc_start: 0.9223 (m-80) cc_final: 0.8698 (m-80) REVERT: A 135 MET cc_start: 0.9244 (mpp) cc_final: 0.8988 (mpp) REVERT: A 167 MET cc_start: 0.9166 (tpp) cc_final: 0.8589 (mmm) REVERT: A 168 LEU cc_start: 0.9828 (tp) cc_final: 0.9591 (tp) REVERT: A 203 MET cc_start: 0.8379 (mpp) cc_final: 0.7779 (mpp) REVERT: A 279 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8688 (mmtt) REVERT: A 348 MET cc_start: 0.9128 (mmp) cc_final: 0.8541 (mmm) REVERT: A 434 LEU cc_start: 0.9325 (tp) cc_final: 0.9081 (tp) REVERT: A 496 ASP cc_start: 0.9185 (t0) cc_final: 0.8947 (t0) REVERT: A 514 MET cc_start: 0.9137 (ptt) cc_final: 0.8607 (ppp) REVERT: B 84 MET cc_start: 0.9401 (pmm) cc_final: 0.8983 (pmm) REVERT: B 212 MET cc_start: 0.9707 (mmp) cc_final: 0.9480 (mmm) REVERT: B 389 MET cc_start: 0.8407 (tpp) cc_final: 0.8147 (tpp) REVERT: B 461 MET cc_start: 0.8831 (ttt) cc_final: 0.8089 (ttt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0769 time to fit residues: 7.6921 Evaluate side-chains 55 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 101 optimal weight: 0.0670 chunk 99 optimal weight: 0.0050 chunk 91 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.029931 restraints weight = 80361.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.030899 restraints weight = 48860.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031581 restraints weight = 35007.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.032049 restraints weight = 27768.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032298 restraints weight = 23612.602| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9714 Z= 0.095 Angle : 0.512 7.626 13233 Z= 0.266 Chirality : 0.041 0.174 1483 Planarity : 0.003 0.040 1615 Dihedral : 17.478 146.689 1495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.82 (0.26), residues: 1112 helix: 1.86 (0.27), residues: 384 sheet: -0.62 (0.36), residues: 182 loop : 0.11 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 489 TYR 0.009 0.001 TYR A 361 PHE 0.009 0.001 PHE B 365 TRP 0.006 0.001 TRP C 82 HIS 0.003 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 9714) covalent geometry : angle 0.51223 / 0.27 (13233) hydrogen bonds : bond 0.02766 / 1.81 ( 390) hydrogen bonds : angle 4.71516 / 3.40 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1404.25 seconds wall clock time: 25 minutes 14.67 seconds (1514.67 seconds total)