Starting phenix.real_space_refine on Wed Aug 5 12:25:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i04_52550/08_2026/9i04_52550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i04_52550/08_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_52550/08_2026/9i04_52550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i04_52550/08_2026/9i04_52550.map" model { file = "/net/cci-nas-00/data/ceres_data/9i04_52550/08_2026/9i04_52550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i04_52550/08_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-2.2rc3-6140/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: 1.45, per 1000 atoms: 0.15 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: 0.79 Conformation dependent library (CDL) restraints added in 287.2 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: 1.01 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: 1.26 Time building geometry restraints manager: 1.02 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: 12844 1.51 - 3.02: 330 3.02 - 4.53: 46 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- 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 : 0.577 7.548 13233 Z= 0.368 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 0.57728 / 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 : 0.335 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: 0.0737 time to fit residues: 7.1860 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 : 0.324 ------------------------------------------------------------------------------- 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 = 0.3032 r_free = 0.3032 target = 0.037436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028656 restraints weight = 85488.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.029594 restraints weight = 51358.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.030233 restraints weight = 36751.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.030684 restraints weight = 29320.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.030974 restraints weight = 25064.188| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9714 Z= 0.165 Angle : 0.555 8.342 13233 Z= 0.296 Chirality : 0.042 0.214 1483 Planarity : 0.004 0.037 1615 Dihedral : 17.447 150.067 1495 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.34 (0.26), residues: 389 sheet: -0.97 (0.36), residues: 180 loop : -0.04 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 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 0.00331 / 0.16 ( 9714) covalent geometry : angle 0.55460 / 0.30 (13233) hydrogen bonds : bond 0.03759 / 2.42 ( 390) hydrogen bonds : angle 5.54096 / 3.99 ( 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 : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9398 (mpp) cc_final: 0.9128 (mpp) REVERT: A 87 PHE cc_start: 0.9453 (m-10) cc_final: 0.8715 (m-80) REVERT: A 168 LEU cc_start: 0.9846 (tp) cc_final: 0.9584 (tp) REVERT: A 203 MET cc_start: 0.8730 (mpp) cc_final: 0.8321 (mpp) REVERT: A 279 LYS cc_start: 0.9357 (mmtt) cc_final: 0.8497 (mmtt) REVERT: A 346 MET cc_start: 0.8848 (tpt) cc_final: 0.8557 (tpp) REVERT: A 348 MET cc_start: 0.9458 (mmp) cc_final: 0.8578 (mmm) REVERT: B 212 MET cc_start: 0.9644 (mmp) cc_final: 0.9427 (mmm) REVERT: B 389 MET cc_start: 0.8381 (tpp) cc_final: 0.8180 (tpp) REVERT: B 461 MET cc_start: 0.8926 (ttt) cc_final: 0.8165 (ttt) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0683 time to fit residues: 6.4659 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 : 0.331 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.036891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.028080 restraints weight = 88238.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029024 restraints weight = 52477.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.029667 restraints weight = 37421.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030095 restraints weight = 29829.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030374 restraints weight = 25615.608| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9714 Z= 0.220 Angle : 0.606 8.221 13233 Z= 0.319 Chirality : 0.042 0.210 1483 Planarity : 0.004 0.037 1615 Dihedral : 17.546 153.658 1495 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 0.28 (0.26), residues: 1112 helix: 1.25 (0.26), residues: 393 sheet: -0.96 (0.38), residues: 169 loop : -0.11 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 43 TYR 0.012 0.002 TYR B 333 PHE 0.011 0.001 PHE A 131 TRP 0.005 0.001 TRP C 82 HIS 0.005 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 ( 9714) covalent geometry : angle 0.60616 / 0.32 (13233) hydrogen bonds : bond 0.03618 / 2.36 ( 390) hydrogen bonds : angle 5.45127 / 3.97 ( 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 61 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9349 (mpp) cc_final: 0.9068 (mpp) REVERT: A 87 PHE cc_start: 0.9494 (m-10) cc_final: 0.8978 (m-80) REVERT: A 135 MET cc_start: 0.8845 (mpp) cc_final: 0.8625 (mpp) REVERT: A 168 LEU cc_start: 0.9846 (tp) cc_final: 0.9562 (tp) REVERT: A 203 MET cc_start: 0.8720 (mpp) cc_final: 0.8290 (mpp) REVERT: A 279 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8558 (mmtt) REVERT: A 348 MET cc_start: 0.9311 (mmp) cc_final: 0.8456 (mmm) REVERT: A 496 ASP cc_start: 0.9211 (t70) cc_final: 0.8991 (t0) REVERT: A 514 MET cc_start: 0.9101 (ptt) cc_final: 0.8605 (ptt) REVERT: B 461 MET cc_start: 0.8937 (ttt) cc_final: 0.8293 (ttt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0669 time to fit residues: 6.3868 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 : 0.347 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** 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 = 0.3049 r_free = 0.3049 target = 0.037967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029023 restraints weight = 83443.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030008 restraints weight = 49686.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030691 restraints weight = 35205.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.031147 restraints weight = 27749.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.031477 restraints weight = 23648.299| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0885 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 : 0.533 7.969 13233 Z= 0.283 Chirality : 0.042 0.198 1483 Planarity : 0.003 0.035 1615 Dihedral : 17.504 151.673 1495 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1112 helix: 1.52 (0.27), residues: 387 sheet: -0.90 (0.37), residues: 175 loop : -0.00 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.009 0.001 TYR B 333 PHE 0.008 0.001 PHE A 350 TRP 0.004 0.001 TRP C 82 HIS 0.002 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 9714) covalent geometry : angle 0.53286 / 0.28 (13233) hydrogen bonds : bond 0.03160 / 2.05 ( 390) hydrogen bonds : angle 5.17402 / 3.75 ( 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 65 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9360 (t0) cc_final: 0.9088 (t70) REVERT: A 62 MET cc_start: 0.9375 (mpp) cc_final: 0.9013 (mmm) REVERT: A 87 PHE cc_start: 0.9463 (m-10) cc_final: 0.8804 (m-80) REVERT: A 168 LEU cc_start: 0.9836 (tp) cc_final: 0.9614 (tp) REVERT: A 279 LYS cc_start: 0.9339 (mmtt) cc_final: 0.8547 (mmtt) REVERT: A 348 MET cc_start: 0.9246 (mmp) cc_final: 0.8602 (mmm) REVERT: A 434 LEU cc_start: 0.9340 (tp) cc_final: 0.9137 (tp) REVERT: A 496 ASP cc_start: 0.9132 (t70) cc_final: 0.8888 (t0) REVERT: B 84 MET cc_start: 0.9502 (pmm) cc_final: 0.9135 (pmm) REVERT: B 212 MET cc_start: 0.9629 (mmp) cc_final: 0.9381 (mmm) REVERT: B 461 MET cc_start: 0.8822 (ttt) cc_final: 0.8149 (ttt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0679 time to fit residues: 6.8772 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 : 0.215 ------------------------------------------------------------------------------- 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: 0.9980 chunk 94 optimal weight: 0.0270 chunk 3 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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** 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 = 0.3065 r_free = 0.3065 target = 0.038408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029481 restraints weight = 83381.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030447 restraints weight = 50661.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.031125 restraints weight = 36303.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031588 restraints weight = 28774.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.031917 restraints weight = 24505.810| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0963 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= 0.101 Angle : 0.518 7.729 13233 Z= 0.273 Chirality : 0.042 0.198 1483 Planarity : 0.003 0.037 1615 Dihedral : 17.475 149.543 1495 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1112 helix: 1.61 (0.27), residues: 389 sheet: -0.76 (0.36), residues: 182 loop : 0.01 (0.29), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 43 TYR 0.011 0.001 TYR B 333 PHE 0.007 0.001 PHE A 60 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 0.00206 / 0.10 ( 9714) covalent geometry : angle 0.51823 / 0.27 (13233) hydrogen bonds : bond 0.03010 / 1.98 ( 390) hydrogen bonds : angle 4.98693 / 3.61 ( 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 68 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9405 (t0) cc_final: 0.9129 (t70) REVERT: A 62 MET cc_start: 0.9377 (mpp) cc_final: 0.9008 (mmm) REVERT: A 87 PHE cc_start: 0.9458 (m-10) cc_final: 0.8793 (m-80) REVERT: A 135 MET cc_start: 0.9269 (mpp) cc_final: 0.8877 (mpp) REVERT: A 168 LEU cc_start: 0.9836 (tp) cc_final: 0.9586 (tp) REVERT: A 279 LYS cc_start: 0.9336 (mmtt) cc_final: 0.8682 (mmtm) REVERT: A 348 MET cc_start: 0.9210 (mmp) cc_final: 0.8549 (mmm) REVERT: A 434 LEU cc_start: 0.9336 (tp) cc_final: 0.9122 (tp) REVERT: A 496 ASP cc_start: 0.9153 (t70) cc_final: 0.8904 (t0) REVERT: B 14 MET cc_start: 0.9178 (tpt) cc_final: 0.8868 (mmm) REVERT: B 84 MET cc_start: 0.9477 (pmm) cc_final: 0.9180 (pmm) REVERT: B 212 MET cc_start: 0.9628 (mmp) cc_final: 0.9389 (mmm) REVERT: B 389 MET cc_start: 0.8226 (tpp) cc_final: 0.7551 (tpp) REVERT: B 461 MET cc_start: 0.8831 (ttt) cc_final: 0.8138 (ttt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0897 time to fit residues: 9.2707 Evaluate side-chains 54 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 0.1980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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 = 0.3067 r_free = 0.3067 target = 0.038617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.029659 restraints weight = 83415.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.030643 restraints weight = 49853.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.031325 restraints weight = 35537.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031776 restraints weight = 28126.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032116 restraints weight = 24004.449| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1070 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= 0.099 Angle : 0.518 7.536 13233 Z= 0.272 Chirality : 0.042 0.193 1483 Planarity : 0.003 0.040 1615 Dihedral : 17.474 148.451 1495 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: 0.64 (0.26), residues: 1112 helix: 1.64 (0.27), residues: 389 sheet: -0.69 (0.36), residues: 182 loop : 0.04 (0.30), residues: 541 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 0.010 0.001 PHE B 365 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 0.00203 / 0.10 ( 9714) covalent geometry : angle 0.51799 / 0.27 (13233) hydrogen bonds : bond 0.02928 / 1.93 ( 390) hydrogen bonds : angle 4.89898 / 3.54 ( 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 66 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.9421 (m-10) cc_final: 0.8790 (m-80) REVERT: A 135 MET cc_start: 0.9256 (mpp) cc_final: 0.8893 (mpp) REVERT: A 168 LEU cc_start: 0.9830 (tp) cc_final: 0.9597 (tp) REVERT: A 279 LYS cc_start: 0.9217 (mmtt) cc_final: 0.8446 (mmtt) REVERT: A 348 MET cc_start: 0.9074 (mmp) cc_final: 0.8544 (mmm) REVERT: A 434 LEU cc_start: 0.9322 (tp) cc_final: 0.9102 (tp) REVERT: A 496 ASP cc_start: 0.9125 (t70) cc_final: 0.8866 (t0) REVERT: A 514 MET cc_start: 0.9075 (ptt) cc_final: 0.8482 (ppp) REVERT: B 14 MET cc_start: 0.9141 (tpt) cc_final: 0.8835 (mmm) REVERT: B 212 MET cc_start: 0.9595 (mmp) cc_final: 0.9363 (mmm) REVERT: B 461 MET cc_start: 0.8784 (ttt) cc_final: 0.8068 (ttt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0897 time to fit residues: 8.9369 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 : 0.362 ------------------------------------------------------------------------------- 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: 7.9990 chunk 112 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 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 = 0.3070 r_free = 0.3070 target = 0.038647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029683 restraints weight = 83305.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030661 restraints weight = 50312.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.031318 restraints weight = 35974.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.031794 restraints weight = 28638.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.032112 restraints weight = 24330.070| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1162 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= 0.106 Angle : 0.520 7.396 13233 Z= 0.272 Chirality : 0.042 0.192 1483 Planarity : 0.003 0.040 1615 Dihedral : 17.465 148.027 1495 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.68 (0.26), residues: 1112 helix: 1.73 (0.27), residues: 384 sheet: -0.66 (0.36), residues: 182 loop : 0.02 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 400 PHE 0.007 0.001 PHE B 59 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 0.00217 / 0.11 ( 9714) covalent geometry : angle 0.52002 / 0.27 (13233) hydrogen bonds : bond 0.02864 / 1.88 ( 390) hydrogen bonds : angle 4.92071 / 3.55 ( 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 66 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9285 (t70) cc_final: 0.8810 (t70) REVERT: A 62 MET cc_start: 0.9366 (mpp) cc_final: 0.9120 (mpp) REVERT: A 87 PHE cc_start: 0.9431 (m-10) cc_final: 0.8776 (m-80) REVERT: A 135 MET cc_start: 0.9254 (mpp) cc_final: 0.8872 (mpp) REVERT: A 168 LEU cc_start: 0.9823 (tp) cc_final: 0.9607 (tp) REVERT: A 279 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8432 (mmtt) REVERT: A 348 MET cc_start: 0.9093 (mmp) cc_final: 0.8530 (mmm) REVERT: A 434 LEU cc_start: 0.9327 (tp) cc_final: 0.9096 (tp) REVERT: A 496 ASP cc_start: 0.9139 (t70) cc_final: 0.8881 (t0) REVERT: A 514 MET cc_start: 0.9081 (ptt) cc_final: 0.8551 (ppp) REVERT: B 84 MET cc_start: 0.9444 (pmm) cc_final: 0.9136 (pmm) REVERT: B 212 MET cc_start: 0.9587 (mmp) cc_final: 0.9370 (mmm) REVERT: B 461 MET cc_start: 0.8782 (ttt) cc_final: 0.8060 (ttt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0990 time to fit residues: 9.7892 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 : 0.374 ------------------------------------------------------------------------------- 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: 8.9990 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 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 = 0.3059 r_free = 0.3059 target = 0.038149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.029218 restraints weight = 83217.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.030177 restraints weight = 50140.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.030840 restraints weight = 35822.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.031311 restraints weight = 28492.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.031625 restraints weight = 24201.246| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9714 Z= 0.123 Angle : 0.524 7.311 13233 Z= 0.274 Chirality : 0.041 0.192 1483 Planarity : 0.004 0.100 1615 Dihedral : 17.477 148.299 1495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: 0.68 (0.26), residues: 1112 helix: 1.74 (0.27), residues: 384 sheet: -0.69 (0.36), residues: 183 loop : 0.03 (0.30), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 43 TYR 0.009 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 0.00252 / 0.12 ( 9714) covalent geometry : angle 0.52352 / 0.27 (13233) hydrogen bonds : bond 0.02908 / 1.93 ( 390) hydrogen bonds : angle 4.89696 / 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 64 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9279 (t70) cc_final: 0.8995 (t70) REVERT: A 62 MET cc_start: 0.9334 (mpp) cc_final: 0.9085 (mpp) REVERT: A 87 PHE cc_start: 0.9426 (m-10) cc_final: 0.8787 (m-80) REVERT: A 135 MET cc_start: 0.9257 (mpp) cc_final: 0.9011 (mmt) REVERT: A 168 LEU cc_start: 0.9822 (tp) cc_final: 0.9618 (tp) REVERT: A 279 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8588 (mmtt) REVERT: A 348 MET cc_start: 0.9106 (mmp) cc_final: 0.8526 (mmm) REVERT: A 434 LEU cc_start: 0.9336 (tp) cc_final: 0.9122 (tp) REVERT: A 496 ASP cc_start: 0.9116 (t70) cc_final: 0.8856 (t0) REVERT: A 514 MET cc_start: 0.9172 (ptt) cc_final: 0.8612 (ppp) REVERT: B 212 MET cc_start: 0.9587 (mmp) cc_final: 0.9377 (mmm) REVERT: B 461 MET cc_start: 0.8781 (ttt) cc_final: 0.8056 (ttt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0830 time to fit residues: 8.3608 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 : 0.337 ------------------------------------------------------------------------------- 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: 0.0170 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 58 optimal weight: 0.2980 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030143 restraints weight = 82022.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.031100 restraints weight = 50123.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.031774 restraints weight = 35995.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.032247 restraints weight = 28603.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.032564 restraints weight = 24298.105| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 9714 Z= 0.101 Angle : 0.536 7.659 13233 Z= 0.277 Chirality : 0.042 0.187 1483 Planarity : 0.004 0.052 1615 Dihedral : 17.459 146.466 1495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 0.72 (0.26), residues: 1112 helix: 1.71 (0.27), residues: 384 sheet: -0.55 (0.36), residues: 182 loop : 0.05 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.010 0.001 TYR A 400 PHE 0.014 0.001 PHE B 135 TRP 0.004 0.001 TRP C 82 HIS 0.002 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 9714) covalent geometry : angle 0.53593 / 0.28 (13233) hydrogen bonds : bond 0.02821 / 1.86 ( 390) hydrogen bonds : angle 4.80803 / 3.47 ( 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 66 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9286 (t70) cc_final: 0.8999 (t70) REVERT: A 87 PHE cc_start: 0.9420 (m-10) cc_final: 0.8883 (m-80) REVERT: A 167 MET cc_start: 0.9162 (tpp) cc_final: 0.8589 (mmm) REVERT: A 168 LEU cc_start: 0.9832 (tp) cc_final: 0.9579 (tp) REVERT: A 203 MET cc_start: 0.8435 (mpp) cc_final: 0.7836 (mpp) REVERT: A 279 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8401 (mmtt) REVERT: A 348 MET cc_start: 0.9122 (mmp) cc_final: 0.8534 (mmm) REVERT: A 434 LEU cc_start: 0.9325 (tp) cc_final: 0.9074 (tp) REVERT: A 496 ASP cc_start: 0.9118 (t70) cc_final: 0.8864 (t0) REVERT: A 514 MET cc_start: 0.9170 (ptt) cc_final: 0.8528 (ppp) REVERT: B 14 MET cc_start: 0.8078 (mmp) cc_final: 0.7305 (mmm) REVERT: B 389 MET cc_start: 0.8418 (mmm) cc_final: 0.8059 (tpp) REVERT: B 461 MET cc_start: 0.8786 (ttt) cc_final: 0.8056 (ttt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0800 time to fit residues: 8.0847 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 : 0.221 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.029239 restraints weight = 84030.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030185 restraints weight = 50610.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.030851 restraints weight = 36210.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.031301 restraints weight = 28772.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031603 restraints weight = 24530.652| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9714 Z= 0.157 Angle : 0.550 7.122 13233 Z= 0.285 Chirality : 0.041 0.192 1483 Planarity : 0.004 0.062 1615 Dihedral : 17.476 147.924 1495 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.76 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: 0.72 (0.27), residues: 1112 helix: 1.77 (0.27), residues: 384 sheet: -0.72 (0.36), residues: 185 loop : 0.07 (0.30), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 489 TYR 0.009 0.001 TYR B 333 PHE 0.008 0.001 PHE B 409 TRP 0.006 0.001 TRP C 82 HIS 0.003 0.001 HIS B 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 9714) covalent geometry : angle 0.55034 / 0.29 (13233) hydrogen bonds : bond 0.02949 / 1.96 ( 390) hydrogen bonds : angle 4.91352 / 3.55 ( 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 62 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.9275 (t70) cc_final: 0.8997 (t0) REVERT: A 87 PHE cc_start: 0.9431 (m-10) cc_final: 0.8931 (m-80) REVERT: A 135 MET cc_start: 0.9187 (mpp) cc_final: 0.8895 (mpp) REVERT: A 167 MET cc_start: 0.9142 (tpp) cc_final: 0.8595 (mmm) REVERT: A 168 LEU cc_start: 0.9821 (tp) cc_final: 0.9587 (tp) REVERT: A 203 MET cc_start: 0.8459 (mpp) cc_final: 0.7868 (mpp) REVERT: A 279 LYS cc_start: 0.9207 (mmtt) cc_final: 0.8649 (mmtp) REVERT: A 348 MET cc_start: 0.9123 (mmp) cc_final: 0.8510 (mmm) REVERT: A 434 LEU cc_start: 0.9349 (tp) cc_final: 0.9149 (tp) REVERT: A 496 ASP cc_start: 0.9127 (t70) cc_final: 0.8872 (t0) REVERT: A 514 MET cc_start: 0.9213 (ptt) cc_final: 0.8540 (ppp) REVERT: B 14 MET cc_start: 0.8171 (mmp) cc_final: 0.7395 (mmm) REVERT: B 20 MET cc_start: 0.7370 (mmp) cc_final: 0.7108 (mmm) REVERT: B 84 MET cc_start: 0.9163 (pmm) cc_final: 0.8781 (pmm) REVERT: B 212 MET cc_start: 0.9689 (mmp) cc_final: 0.9472 (mmm) REVERT: B 461 MET cc_start: 0.8814 (ttt) cc_final: 0.8090 (ttt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0751 time to fit residues: 7.2642 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 : 0.377 ------------------------------------------------------------------------------- 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: 0.8980 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.038482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.029585 restraints weight = 82172.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.030553 restraints weight = 49482.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.031221 restraints weight = 35375.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.031680 restraints weight = 28074.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.032007 restraints weight = 23897.124| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 9714 Z= 0.111 Angle : 0.531 7.959 13233 Z= 0.274 Chirality : 0.042 0.186 1483 Planarity : 0.004 0.045 1615 Dihedral : 17.469 147.660 1495 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.78 (0.27), residues: 1112 helix: 1.79 (0.27), residues: 384 sheet: -0.59 (0.36), residues: 182 loop : 0.10 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 400 PHE 0.008 0.001 PHE A 60 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 0.00238 / 0.11 ( 9714) covalent geometry : angle 0.53105 / 0.27 (13233) hydrogen bonds : bond 0.02849 / 1.88 ( 390) hydrogen bonds : angle 4.83059 / 3.48 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1361.48 seconds wall clock time: 24 minutes 26.06 seconds (1466.06 seconds total)