Starting phenix.real_space_refine on Wed Aug 5 02:24:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30bu_57549/08_2026/30bu_57549.cif Found real_map, /net/cci-nas-00/data/ceres_data/30bu_57549/08_2026/30bu_57549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30bu_57549/08_2026/30bu_57549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30bu_57549/08_2026/30bu_57549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30bu_57549/08_2026/30bu_57549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30bu_57549/08_2026/30bu_57549.map" } resolution = 4.1 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= 0.003 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 5233 2.51 5 N 1354 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 7929 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4105 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 31, 'TRANS': 496} Chain: "B" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3824 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 29, 'TRANS': 466} Time building chain proxies: 1.84, per 1000 atoms: 0.23 Number of scatterers: 7929 At special positions: 0 Unit cell: (88.044, 77.924, 140.668, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1326 8.00 N 1354 7.00 C 5233 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: 0.45 Conformation dependent library (CDL) restraints added in 402.7 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 69.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 3.718A pdb=" N VAL A 9 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.736A pdb=" N ALA A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 199 through 220 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 240 through 250 Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.081A pdb=" N PHE A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 removed outlier: 4.065A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 4.196A pdb=" N PHE A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 321 Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.532A pdb=" N LEU A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.562A pdb=" N TYR A 347 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 372 Proline residue: A 366 - end of helix Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 379 through 401 removed outlier: 3.510A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Proline residue: A 385 - end of helix Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 406 through 433 removed outlier: 3.800A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.540A pdb=" N ALA A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.778A pdb=" N LEU A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 494 removed outlier: 3.532A pdb=" N TRP A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 507 through 527 removed outlier: 3.915A pdb=" N LEU A 511 " --> pdb=" O HIS A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.799A pdb=" N ARG B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 26 through 45 Processing helix chain 'B' and resid 52 through 76 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 199 through 220 removed outlier: 3.581A pdb=" N ARG B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 234 removed outlier: 5.653A pdb=" N ILE B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.996A pdb=" N THR B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 4.004A pdb=" N PHE B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 278 removed outlier: 4.828A pdb=" N VAL B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.574A pdb=" N THR B 299 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 322 Processing helix chain 'B' and resid 323 through 342 removed outlier: 3.717A pdb=" N PHE B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR B 328 " --> pdb=" O GLN B 324 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.966A pdb=" N TYR B 347 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.620A pdb=" N VAL B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 379 through 401 removed outlier: 3.532A pdb=" N VAL B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Proline residue: B 385 - end of helix Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 406 through 435 removed outlier: 3.573A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 445 removed outlier: 4.179A pdb=" N ALA B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 463 removed outlier: 3.745A pdb=" N VAL B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 494 removed outlier: 3.665A pdb=" N TYR B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 485 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 94 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 87 through 94 current: chain 'A' and resid 104 through 116 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 121 current: chain 'A' and resid 181 through 184 Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 94 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 89 through 94 current: chain 'B' and resid 104 through 116 removed outlier: 5.453A pdb=" N ARG B 104 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 131 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B 106 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 108 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 127 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA B 110 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU B 125 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 112 " --> pdb=" O VAL B 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 119 through 131 current: chain 'B' and resid 181 through 184 Processing sheet with id=AA4, first strand: chain 'B' and resid 402 through 404 482 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2503 1.34 - 1.46: 1783 1.46 - 1.58: 3818 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 8132 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.81e-01 bond pdb=" C PRO B 47 " pdb=" N PRO B 48 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.75e-01 bond pdb=" N VAL B 196 " pdb=" CA VAL B 196 " ideal model delta sigma weight residual 1.454 1.460 -0.006 7.70e-03 1.69e+04 5.94e-01 bond pdb=" CB GLN B 46 " pdb=" CG GLN B 46 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.67e-01 bond pdb=" CA VAL A 252 " pdb=" CB VAL A 252 " ideal model delta sigma weight residual 1.539 1.549 -0.009 1.27e-02 6.20e+03 5.35e-01 ... (remaining 8127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10841 1.49 - 2.98: 218 2.98 - 4.47: 43 4.47 - 5.96: 15 5.96 - 7.45: 6 Bond angle restraints: 11123 Sorted by residual: angle pdb=" N PRO B 47 " pdb=" CA PRO B 47 " pdb=" C PRO B 47 " ideal model delta sigma weight residual 110.70 114.34 -3.64 1.22e+00 6.72e-01 8.92e+00 angle pdb=" CA LYS B 192 " pdb=" CB LYS B 192 " pdb=" CG LYS B 192 " ideal model delta sigma weight residual 114.10 118.54 -4.44 2.00e+00 2.50e-01 4.93e+00 angle pdb=" CB ARG B 489 " pdb=" CG ARG B 489 " pdb=" CD ARG B 489 " ideal model delta sigma weight residual 111.30 116.39 -5.09 2.30e+00 1.89e-01 4.91e+00 angle pdb=" CA LEU A 454 " pdb=" CB LEU A 454 " pdb=" CG LEU A 454 " ideal model delta sigma weight residual 116.30 123.75 -7.45 3.50e+00 8.16e-02 4.53e+00 angle pdb=" CA LEU B 206 " pdb=" CB LEU B 206 " pdb=" CG LEU B 206 " ideal model delta sigma weight residual 116.30 123.75 -7.45 3.50e+00 8.16e-02 4.53e+00 ... (remaining 11118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 4443 15.93 - 31.87: 257 31.87 - 47.80: 50 47.80 - 63.74: 9 63.74 - 79.67: 7 Dihedral angle restraints: 4766 sinusoidal: 1805 harmonic: 2961 Sorted by residual: dihedral pdb=" CA PRO A 221 " pdb=" C PRO A 221 " pdb=" N PRO A 222 " pdb=" CA PRO A 222 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA VAL B 362 " pdb=" C VAL B 362 " pdb=" N TYR B 363 " pdb=" CA TYR B 363 " ideal model delta harmonic sigma weight residual -180.00 -163.94 -16.06 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ASP A 370 " pdb=" CB ASP A 370 " pdb=" CG ASP A 370 " pdb=" OD1 ASP A 370 " ideal model delta sinusoidal sigma weight residual -30.00 -81.91 51.91 1 2.00e+01 2.50e-03 9.19e+00 ... (remaining 4763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 804 0.029 - 0.057: 336 0.057 - 0.086: 102 0.086 - 0.115: 67 0.115 - 0.143: 11 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA PRO A 222 " pdb=" N PRO A 222 " pdb=" C PRO A 222 " pdb=" CB PRO A 222 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 178 " pdb=" N ILE A 178 " pdb=" C ILE A 178 " pdb=" CB ILE A 178 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1317 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 443 " -0.011 2.00e-02 2.50e+03 1.25e-02 2.72e+00 pdb=" CG PHE A 443 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 443 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 443 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 443 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 443 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 443 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 375 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 376 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 355 " 0.012 2.00e-02 2.50e+03 1.10e-02 2.11e+00 pdb=" CG PHE A 355 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 355 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 355 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 355 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 355 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 355 " 0.000 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.07: 5378 3.07 - 3.53: 8596 3.53 - 3.99: 11523 3.99 - 4.44: 13830 4.44 - 4.90: 20991 Nonbonded interactions: 60318 Sorted by model distance: nonbonded pdb=" O ASN B 103 " pdb=" OD1 ASN B 103 " model vdw 2.618 3.040 nonbonded pdb=" O LEU B 431 " pdb=" O THR B 435 " model vdw 2.640 3.040 nonbonded pdb=" O ASP A 326 " pdb=" OD1 ASP A 326 " model vdw 2.652 3.040 nonbonded pdb=" O THR A 472 " pdb=" OG1 THR A 472 " model vdw 2.653 3.040 nonbonded pdb=" O GLY B 447 " pdb=" OD1 ASN B 451 " model vdw 2.659 3.040 ... (remaining 60313 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 496) selection = chain 'B' } 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.800 Find NCS groups from input model: 0.130 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.002 0.034 8132 Z= 0.106 Angle : 0.562 7.448 11123 Z= 0.272 Chirality : 0.040 0.143 1320 Planarity : 0.004 0.041 1385 Dihedral : 10.997 79.672 2872 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.27), residues: 1020 helix: 1.52 (0.20), residues: 650 sheet: -0.60 (0.60), residues: 59 loop : 0.44 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.011 0.001 TYR B 363 PHE 0.029 0.001 PHE A 443 TRP 0.023 0.002 TRP A 506 HIS 0.007 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 8132) covalent geometry : angle 0.56201 / 0.27 (11123) hydrogen bonds : bond 0.15704 / 11.14 ( 482) hydrogen bonds : angle 5.85897 / 4.63 ( 1431) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8601 (mt) cc_final: 0.8282 (tt) REVERT: A 49 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7279 (mmt90) REVERT: A 96 GLU cc_start: 0.8657 (pm20) cc_final: 0.8399 (pm20) REVERT: A 126 LYS cc_start: 0.8001 (mttt) cc_final: 0.7668 (mmtt) REVERT: A 182 MET cc_start: 0.7212 (tpp) cc_final: 0.6844 (mmt) REVERT: A 375 LEU cc_start: 0.7925 (mt) cc_final: 0.7559 (mp) REVERT: A 491 PHE cc_start: 0.8909 (t80) cc_final: 0.8481 (t80) REVERT: B 1 MET cc_start: 0.6288 (tmm) cc_final: 0.5496 (tmm) REVERT: B 49 ARG cc_start: 0.6562 (ttt-90) cc_final: 0.6069 (ttt-90) REVERT: B 150 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7926 (ttp80) REVERT: B 170 ARG cc_start: 0.8736 (mtt-85) cc_final: 0.8174 (tpp80) REVERT: B 199 HIS cc_start: 0.7185 (t-90) cc_final: 0.6887 (m-70) REVERT: B 359 TRP cc_start: 0.7002 (t-100) cc_final: 0.5493 (t-100) REVERT: B 389 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8699 (tp-100) REVERT: B 456 PHE cc_start: 0.8647 (m-10) cc_final: 0.8363 (m-80) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.0718 time to fit residues: 21.3114 Evaluate side-chains 162 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 HIS A 128 GLN A 199 HIS A 401 ASN B 185 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.170086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137812 restraints weight = 14717.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141648 restraints weight = 8574.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144222 restraints weight = 6049.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145782 restraints weight = 4818.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.146961 restraints weight = 4185.279| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8132 Z= 0.126 Angle : 0.526 6.404 11123 Z= 0.261 Chirality : 0.040 0.144 1320 Planarity : 0.004 0.038 1385 Dihedral : 3.369 18.935 1141 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.12 % Allowed : 2.36 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 1020 helix: 1.80 (0.20), residues: 663 sheet: -0.55 (0.61), residues: 59 loop : 0.53 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.013 0.001 TYR B 363 PHE 0.013 0.001 PHE A 355 TRP 0.013 0.001 TRP A 506 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 8132) covalent geometry : angle 0.52633 / 0.26 (11123) hydrogen bonds : bond 0.04228 / 2.83 ( 482) hydrogen bonds : angle 4.47718 / 3.43 ( 1431) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8682 (mt) cc_final: 0.8350 (tt) REVERT: A 62 MET cc_start: 0.7860 (tpp) cc_final: 0.7609 (tpp) REVERT: A 96 GLU cc_start: 0.8477 (pm20) cc_final: 0.8133 (pm20) REVERT: A 126 LYS cc_start: 0.7709 (mttt) cc_final: 0.7344 (mmtt) REVERT: A 182 MET cc_start: 0.6736 (tpp) cc_final: 0.6348 (mmt) REVERT: A 347 TYR cc_start: 0.8436 (m-80) cc_final: 0.8176 (m-10) REVERT: A 456 PHE cc_start: 0.8136 (t80) cc_final: 0.7661 (t80) REVERT: B 49 ARG cc_start: 0.6234 (ttt-90) cc_final: 0.5932 (ttt-90) REVERT: B 150 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7517 (ttp80) REVERT: B 170 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.7911 (tpp80) REVERT: B 182 MET cc_start: 0.8372 (ttm) cc_final: 0.8127 (ttm) REVERT: B 389 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8319 (tp-100) REVERT: B 393 LEU cc_start: 0.9006 (tp) cc_final: 0.8728 (tp) REVERT: B 452 LEU cc_start: 0.8729 (mt) cc_final: 0.8527 (mt) REVERT: B 456 PHE cc_start: 0.7995 (m-10) cc_final: 0.7760 (m-80) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.0725 time to fit residues: 20.7806 Evaluate side-chains 164 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 152 HIS A 199 HIS A 401 ASN B 185 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.165872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131351 restraints weight = 15565.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134763 restraints weight = 9795.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.137029 restraints weight = 7255.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138262 restraints weight = 6000.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139302 restraints weight = 5372.958| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8132 Z= 0.223 Angle : 0.633 6.516 11123 Z= 0.322 Chirality : 0.043 0.142 1320 Planarity : 0.005 0.039 1385 Dihedral : 3.708 20.534 1141 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.37 % Allowed : 3.36 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.27), residues: 1020 helix: 1.77 (0.20), residues: 645 sheet: -0.71 (0.60), residues: 68 loop : 0.54 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 489 TYR 0.028 0.002 TYR A 365 PHE 0.023 0.002 PHE A 355 TRP 0.022 0.002 TRP A 488 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 ( 8132) covalent geometry : angle 0.63267 / 0.32 (11123) hydrogen bonds : bond 0.04559 / 3.06 ( 482) hydrogen bonds : angle 4.64754 / 3.48 ( 1431) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 199 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8701 (mt) cc_final: 0.8449 (tt) REVERT: A 126 LYS cc_start: 0.7808 (mttt) cc_final: 0.7551 (mmtt) REVERT: A 163 ASN cc_start: 0.9189 (t0) cc_final: 0.8957 (t0) REVERT: A 316 LEU cc_start: 0.8636 (tp) cc_final: 0.8383 (tp) REVERT: A 456 PHE cc_start: 0.8171 (t80) cc_final: 0.7702 (t80) REVERT: A 463 LEU cc_start: 0.8070 (tp) cc_final: 0.7620 (tt) REVERT: A 489 ARG cc_start: 0.8323 (tpt-90) cc_final: 0.7893 (tmm-80) REVERT: B 49 ARG cc_start: 0.6309 (ttt-90) cc_final: 0.5990 (ttt-90) REVERT: B 170 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.8093 (tpp80) REVERT: B 233 PHE cc_start: 0.7511 (m-80) cc_final: 0.7301 (m-80) REVERT: B 328 TYR cc_start: 0.8162 (m-80) cc_final: 0.7400 (m-80) REVERT: B 363 TYR cc_start: 0.8702 (t80) cc_final: 0.8104 (t80) REVERT: B 389 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8155 (tp-100) REVERT: B 393 LEU cc_start: 0.9128 (tp) cc_final: 0.8800 (tp) REVERT: B 456 PHE cc_start: 0.8122 (m-10) cc_final: 0.7855 (m-80) outliers start: 3 outliers final: 0 residues processed: 199 average time/residue: 0.0775 time to fit residues: 21.1138 Evaluate side-chains 160 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 401 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132225 restraints weight = 16005.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135592 restraints weight = 10298.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139034 restraints weight = 6870.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139315 restraints weight = 5692.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139291 restraints weight = 5285.960| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8132 Z= 0.183 Angle : 0.604 9.843 11123 Z= 0.301 Chirality : 0.042 0.178 1320 Planarity : 0.004 0.040 1385 Dihedral : 3.772 19.872 1141 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.27), residues: 1020 helix: 1.75 (0.20), residues: 645 sheet: -0.39 (0.61), residues: 76 loop : 0.34 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.017 0.001 TYR B 398 PHE 0.020 0.002 PHE B 233 TRP 0.014 0.002 TRP A 506 HIS 0.009 0.001 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 8132) covalent geometry : angle 0.60404 / 0.30 (11123) hydrogen bonds : bond 0.04222 / 2.83 ( 482) hydrogen bonds : angle 4.50147 / 3.38 ( 1431) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8695 (mt) cc_final: 0.8475 (tt) REVERT: A 49 ARG cc_start: 0.5686 (mmt90) cc_final: 0.5448 (mmt90) REVERT: A 96 GLU cc_start: 0.8319 (pm20) cc_final: 0.7955 (pm20) REVERT: A 126 LYS cc_start: 0.7897 (mttt) cc_final: 0.7636 (mmtt) REVERT: A 172 TYR cc_start: 0.8420 (t80) cc_final: 0.8194 (t80) REVERT: A 182 MET cc_start: 0.7299 (mmm) cc_final: 0.7051 (mmm) REVERT: A 233 PHE cc_start: 0.8287 (m-80) cc_final: 0.8069 (m-10) REVERT: A 316 LEU cc_start: 0.8454 (tp) cc_final: 0.8198 (tp) REVERT: A 456 PHE cc_start: 0.8333 (t80) cc_final: 0.7840 (t80) REVERT: A 489 ARG cc_start: 0.8261 (tpt-90) cc_final: 0.7744 (tmm160) REVERT: B 1 MET cc_start: 0.7099 (tmm) cc_final: 0.6346 (tmm) REVERT: B 49 ARG cc_start: 0.6352 (ttt-90) cc_final: 0.6129 (ttt-90) REVERT: B 95 ILE cc_start: 0.9278 (tp) cc_final: 0.9051 (tp) REVERT: B 170 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.8069 (tpp80) REVERT: B 328 TYR cc_start: 0.8070 (m-80) cc_final: 0.7382 (m-80) REVERT: B 363 TYR cc_start: 0.8738 (t80) cc_final: 0.8175 (t80) REVERT: B 389 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8142 (tp-100) REVERT: B 393 LEU cc_start: 0.9086 (tp) cc_final: 0.8777 (tp) REVERT: B 456 PHE cc_start: 0.8170 (m-10) cc_final: 0.7920 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.0778 time to fit residues: 20.7747 Evaluate side-chains 149 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 501 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134751 restraints weight = 15878.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138673 restraints weight = 9476.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141247 restraints weight = 6816.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142818 restraints weight = 5527.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144112 restraints weight = 4858.399| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8132 Z= 0.120 Angle : 0.546 8.991 11123 Z= 0.266 Chirality : 0.040 0.155 1320 Planarity : 0.004 0.040 1385 Dihedral : 3.618 17.628 1141 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.27), residues: 1020 helix: 1.97 (0.21), residues: 645 sheet: -0.51 (0.54), residues: 89 loop : 0.43 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.020 0.001 TYR A 365 PHE 0.024 0.002 PHE B 56 TRP 0.017 0.001 TRP A 506 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8132) covalent geometry : angle 0.54556 / 0.27 (11123) hydrogen bonds : bond 0.03846 / 2.55 ( 482) hydrogen bonds : angle 4.25390 / 3.20 ( 1431) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8702 (mt) cc_final: 0.8464 (tt) REVERT: A 49 ARG cc_start: 0.5875 (mmt90) cc_final: 0.5568 (mmt90) REVERT: A 66 LEU cc_start: 0.7813 (tp) cc_final: 0.7603 (tt) REVERT: A 172 TYR cc_start: 0.8286 (t80) cc_final: 0.8047 (t80) REVERT: A 182 MET cc_start: 0.7290 (mmm) cc_final: 0.6957 (mmm) REVERT: A 233 PHE cc_start: 0.8205 (m-80) cc_final: 0.7956 (m-10) REVERT: A 316 LEU cc_start: 0.8400 (tp) cc_final: 0.8129 (tp) REVERT: B 1 MET cc_start: 0.7057 (tmm) cc_final: 0.6288 (tmm) REVERT: B 49 ARG cc_start: 0.6453 (ttt-90) cc_final: 0.5235 (ttp80) REVERT: B 95 ILE cc_start: 0.9260 (tp) cc_final: 0.9017 (tp) REVERT: B 162 ARG cc_start: 0.3459 (tmt170) cc_final: 0.2128 (ttp-170) REVERT: B 170 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.8011 (tpp80) REVERT: B 232 LEU cc_start: 0.8311 (tt) cc_final: 0.7985 (pp) REVERT: B 328 TYR cc_start: 0.8023 (m-80) cc_final: 0.7214 (m-80) REVERT: B 389 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8119 (tp-100) REVERT: B 393 LEU cc_start: 0.8989 (tp) cc_final: 0.8674 (tp) REVERT: B 456 PHE cc_start: 0.8090 (m-10) cc_final: 0.7879 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.0859 time to fit residues: 22.8762 Evaluate side-chains 148 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 401 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.167279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134386 restraints weight = 14854.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138174 restraints weight = 8698.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140680 restraints weight = 6139.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142222 restraints weight = 4907.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143301 restraints weight = 4272.773| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8132 Z= 0.131 Angle : 0.561 9.012 11123 Z= 0.272 Chirality : 0.041 0.175 1320 Planarity : 0.004 0.040 1385 Dihedral : 3.611 15.603 1141 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 1.88 (0.27), residues: 1020 helix: 1.92 (0.21), residues: 645 sheet: -0.64 (0.57), residues: 79 loop : 0.44 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.021 0.001 TYR B 398 PHE 0.021 0.002 PHE A 351 TRP 0.017 0.001 TRP A 506 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8132) covalent geometry : angle 0.56132 / 0.27 (11123) hydrogen bonds : bond 0.03866 / 2.58 ( 482) hydrogen bonds : angle 4.25370 / 3.18 ( 1431) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8769 (mt) cc_final: 0.8553 (tt) REVERT: A 66 LEU cc_start: 0.7695 (tp) cc_final: 0.7440 (tt) REVERT: A 172 TYR cc_start: 0.8369 (t80) cc_final: 0.8104 (t80) REVERT: A 182 MET cc_start: 0.7284 (mmm) cc_final: 0.6957 (mmm) REVERT: A 193 LEU cc_start: 0.8029 (mp) cc_final: 0.7798 (tp) REVERT: A 316 LEU cc_start: 0.8457 (tp) cc_final: 0.8210 (tp) REVERT: B 1 MET cc_start: 0.6901 (tmm) cc_final: 0.6135 (tmm) REVERT: B 49 ARG cc_start: 0.6464 (ttt-90) cc_final: 0.5265 (ttp80) REVERT: B 95 ILE cc_start: 0.9263 (tp) cc_final: 0.9025 (tp) REVERT: B 162 ARG cc_start: 0.3429 (tmt170) cc_final: 0.2035 (ttp-170) REVERT: B 265 LEU cc_start: 0.8860 (mm) cc_final: 0.8655 (mm) REVERT: B 328 TYR cc_start: 0.8055 (m-80) cc_final: 0.7327 (m-80) REVERT: B 389 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8069 (tp-100) REVERT: B 393 LEU cc_start: 0.9038 (tp) cc_final: 0.8727 (tp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0742 time to fit residues: 20.4946 Evaluate side-chains 149 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 28 optimal weight: 0.0000 chunk 65 optimal weight: 0.5980 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 199 HIS B 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138142 restraints weight = 15825.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142190 restraints weight = 9375.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144878 restraints weight = 6678.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146349 restraints weight = 5373.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147627 restraints weight = 4720.867| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8132 Z= 0.110 Angle : 0.556 10.316 11123 Z= 0.267 Chirality : 0.041 0.166 1320 Planarity : 0.004 0.058 1385 Dihedral : 3.655 30.992 1141 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.27), residues: 1020 helix: 1.85 (0.21), residues: 650 sheet: -0.66 (0.57), residues: 79 loop : 0.46 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 223 TYR 0.020 0.001 TYR B 398 PHE 0.028 0.001 PHE B 456 TRP 0.029 0.002 TRP A 504 HIS 0.006 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 8132) covalent geometry : angle 0.55626 / 0.27 (11123) hydrogen bonds : bond 0.03727 / 2.47 ( 482) hydrogen bonds : angle 4.15091 / 3.10 ( 1431) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7560 (tp) cc_final: 0.7335 (tt) REVERT: A 182 MET cc_start: 0.7251 (mmm) cc_final: 0.6897 (mmm) REVERT: A 193 LEU cc_start: 0.8144 (mp) cc_final: 0.7926 (tp) REVERT: A 316 LEU cc_start: 0.8348 (tp) cc_final: 0.8069 (tp) REVERT: B 1 MET cc_start: 0.6911 (tmm) cc_final: 0.6109 (tmm) REVERT: B 49 ARG cc_start: 0.6403 (ttt-90) cc_final: 0.5256 (ttp80) REVERT: B 95 ILE cc_start: 0.9196 (tp) cc_final: 0.8946 (tp) REVERT: B 162 ARG cc_start: 0.3350 (tmt170) cc_final: 0.2041 (ttp-170) REVERT: B 265 LEU cc_start: 0.8820 (mm) cc_final: 0.8614 (mm) REVERT: B 389 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8058 (tp-100) REVERT: B 393 LEU cc_start: 0.8958 (tp) cc_final: 0.8674 (tp) REVERT: B 456 PHE cc_start: 0.7991 (m-80) cc_final: 0.7673 (m-80) REVERT: B 470 LEU cc_start: 0.8114 (mt) cc_final: 0.7904 (mt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0715 time to fit residues: 20.2559 Evaluate side-chains 155 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 87 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137430 restraints weight = 14931.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141237 restraints weight = 8850.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143894 restraints weight = 6270.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145576 restraints weight = 4971.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146744 restraints weight = 4283.205| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8132 Z= 0.106 Angle : 0.548 11.101 11123 Z= 0.263 Chirality : 0.041 0.182 1320 Planarity : 0.004 0.038 1385 Dihedral : 3.567 22.763 1141 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.27), residues: 1020 helix: 1.84 (0.21), residues: 655 sheet: -0.70 (0.57), residues: 79 loop : 0.52 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 321 TYR 0.020 0.001 TYR B 398 PHE 0.023 0.001 PHE B 456 TRP 0.019 0.001 TRP A 506 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 8132) covalent geometry : angle 0.54750 / 0.26 (11123) hydrogen bonds : bond 0.03574 / 2.38 ( 482) hydrogen bonds : angle 4.12575 / 3.07 ( 1431) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7653 (tp) cc_final: 0.7389 (tt) REVERT: A 170 ARG cc_start: 0.8333 (ttm110) cc_final: 0.8022 (ttm110) REVERT: A 182 MET cc_start: 0.7328 (mmm) cc_final: 0.6978 (mmm) REVERT: A 193 LEU cc_start: 0.8039 (mp) cc_final: 0.7808 (tp) REVERT: A 316 LEU cc_start: 0.8523 (tp) cc_final: 0.8248 (tp) REVERT: B 1 MET cc_start: 0.6984 (tmm) cc_final: 0.6211 (tmm) REVERT: B 95 ILE cc_start: 0.9189 (tp) cc_final: 0.8940 (tp) REVERT: B 96 GLU cc_start: 0.7933 (tp30) cc_final: 0.7410 (tp30) REVERT: B 162 ARG cc_start: 0.3463 (tmt170) cc_final: 0.2150 (ttp-170) REVERT: B 328 TYR cc_start: 0.7962 (m-80) cc_final: 0.7264 (m-80) REVERT: B 389 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8016 (tp-100) REVERT: B 393 LEU cc_start: 0.8943 (tp) cc_final: 0.8632 (tp) REVERT: B 456 PHE cc_start: 0.7867 (m-80) cc_final: 0.7547 (m-80) REVERT: B 470 LEU cc_start: 0.8098 (mt) cc_final: 0.7890 (mt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0788 time to fit residues: 21.5632 Evaluate side-chains 152 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.172542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.138107 restraints weight = 15563.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141953 restraints weight = 10618.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146419 restraints weight = 6941.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146370 restraints weight = 5543.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146366 restraints weight = 5182.304| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8132 Z= 0.108 Angle : 0.552 11.330 11123 Z= 0.264 Chirality : 0.041 0.176 1320 Planarity : 0.004 0.037 1385 Dihedral : 3.531 21.723 1141 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.27), residues: 1020 helix: 1.84 (0.21), residues: 657 sheet: -0.68 (0.54), residues: 89 loop : 0.47 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 489 TYR 0.020 0.001 TYR B 398 PHE 0.024 0.001 PHE A 355 TRP 0.019 0.001 TRP A 506 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 8132) covalent geometry : angle 0.55170 / 0.26 (11123) hydrogen bonds : bond 0.03496 / 2.34 ( 482) hydrogen bonds : angle 4.08464 / 3.04 ( 1431) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7569 (tp) cc_final: 0.7300 (tt) REVERT: A 170 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8056 (ttm110) REVERT: A 172 TYR cc_start: 0.8262 (t80) cc_final: 0.7963 (t80) REVERT: A 182 MET cc_start: 0.7440 (mmm) cc_final: 0.7078 (mmm) REVERT: A 316 LEU cc_start: 0.8390 (tp) cc_final: 0.8116 (tp) REVERT: B 1 MET cc_start: 0.6944 (tmm) cc_final: 0.6168 (tmm) REVERT: B 95 ILE cc_start: 0.9194 (tp) cc_final: 0.8926 (tp) REVERT: B 96 GLU cc_start: 0.7800 (tp30) cc_final: 0.7417 (tp30) REVERT: B 97 GLU cc_start: 0.8039 (pt0) cc_final: 0.7448 (mt-10) REVERT: B 265 LEU cc_start: 0.8761 (mm) cc_final: 0.8547 (mm) REVERT: B 328 TYR cc_start: 0.8051 (m-80) cc_final: 0.7350 (m-80) REVERT: B 389 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8076 (tp-100) REVERT: B 393 LEU cc_start: 0.8935 (tp) cc_final: 0.8642 (tp) REVERT: B 456 PHE cc_start: 0.8097 (m-80) cc_final: 0.7744 (m-80) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0624 time to fit residues: 17.5634 Evaluate side-chains 152 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 HIS A 199 HIS B 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.172229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137649 restraints weight = 15753.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141482 restraints weight = 10709.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146419 restraints weight = 6941.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146245 restraints weight = 5490.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146195 restraints weight = 5056.699| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8132 Z= 0.105 Angle : 0.533 6.356 11123 Z= 0.258 Chirality : 0.040 0.143 1320 Planarity : 0.004 0.037 1385 Dihedral : 3.497 21.006 1141 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.27), residues: 1020 helix: 1.81 (0.20), residues: 657 sheet: -0.71 (0.57), residues: 79 loop : 0.43 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 112 TYR 0.021 0.001 TYR B 398 PHE 0.023 0.001 PHE A 355 TRP 0.020 0.001 TRP A 506 HIS 0.006 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 8132) covalent geometry : angle 0.53263 / 0.26 (11123) hydrogen bonds : bond 0.03456 / 2.30 ( 482) hydrogen bonds : angle 4.05460 / 3.01 ( 1431) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7623 (tp) cc_final: 0.7342 (tt) REVERT: A 170 ARG cc_start: 0.8359 (ttm110) cc_final: 0.8060 (ttm110) REVERT: A 172 TYR cc_start: 0.8277 (t80) cc_final: 0.7973 (t80) REVERT: A 182 MET cc_start: 0.7474 (mmm) cc_final: 0.7107 (mmm) REVERT: A 316 LEU cc_start: 0.8377 (tp) cc_final: 0.8108 (tp) REVERT: B 1 MET cc_start: 0.6976 (tmm) cc_final: 0.6182 (tmm) REVERT: B 21 SER cc_start: 0.8606 (t) cc_final: 0.8283 (m) REVERT: B 95 ILE cc_start: 0.9155 (tp) cc_final: 0.8918 (tp) REVERT: B 96 GLU cc_start: 0.7842 (tp30) cc_final: 0.7420 (tp30) REVERT: B 97 GLU cc_start: 0.8119 (pt0) cc_final: 0.7118 (mt-10) REVERT: B 162 ARG cc_start: 0.3680 (ttt-90) cc_final: 0.2991 (ttp-170) REVERT: B 265 LEU cc_start: 0.8758 (mm) cc_final: 0.8549 (mm) REVERT: B 328 TYR cc_start: 0.8054 (m-80) cc_final: 0.7334 (m-80) REVERT: B 359 TRP cc_start: 0.6728 (t-100) cc_final: 0.5323 (t-100) REVERT: B 389 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8059 (tp-100) REVERT: B 393 LEU cc_start: 0.8963 (tp) cc_final: 0.8679 (tp) REVERT: B 456 PHE cc_start: 0.8147 (m-80) cc_final: 0.7795 (m-80) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.0700 time to fit residues: 18.8391 Evaluate side-chains 147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 0.0170 chunk 65 optimal weight: 0.0570 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 HIS A 199 HIS B 185 ASN B 324 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139819 restraints weight = 15644.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143669 restraints weight = 10700.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146779 restraints weight = 7053.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147468 restraints weight = 5964.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147208 restraints weight = 5315.054| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8132 Z= 0.100 Angle : 0.549 12.206 11123 Z= 0.259 Chirality : 0.040 0.176 1320 Planarity : 0.004 0.038 1385 Dihedral : 3.463 19.869 1141 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.27), residues: 1020 helix: 1.85 (0.21), residues: 656 sheet: -0.49 (0.54), residues: 89 loop : 0.49 (0.42), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.018 0.001 TYR B 398 PHE 0.022 0.001 PHE B 456 TRP 0.020 0.001 TRP A 506 HIS 0.006 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 8132) covalent geometry : angle 0.54852 / 0.26 (11123) hydrogen bonds : bond 0.03367 / 2.25 ( 482) hydrogen bonds : angle 3.99661 / 2.97 ( 1431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1307.19 seconds wall clock time: 23 minutes 4.38 seconds (1384.38 seconds total)