Starting phenix.real_space_refine on Sat Aug 23 06:42:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0s_39714/08_2025/8z0s_39714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0s_39714/08_2025/8z0s_39714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0s_39714/08_2025/8z0s_39714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0s_39714/08_2025/8z0s_39714.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0s_39714/08_2025/8z0s_39714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0s_39714/08_2025/8z0s_39714.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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 24 5.16 5 C 6553 2.51 5 N 1851 2.21 5 O 1905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10333 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3452 Classifications: {'peptide': 443} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 412} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3398 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 29, 'TRANS': 408} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 7 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3483 Classifications: {'peptide': 446} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 415} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 2.83, per 1000 atoms: 0.27 Number of scatterers: 10333 At special positions: 0 Unit cell: (96.6, 99.96, 134.4, 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 24 16.00 O 1905 8.00 N 1851 7.00 C 6553 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: 0.98 Conformation dependent library (CDL) restraints added in 446.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 40.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.789A pdb=" N SER B 117 " --> pdb=" O CYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 193 through 206 removed outlier: 4.178A pdb=" N ALA B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 261 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 430 through 439 removed outlier: 3.657A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 533 removed outlier: 3.601A pdb=" N LEU B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 547 removed outlier: 3.746A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 removed outlier: 4.095A pdb=" N GLU C 118 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 119 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 242 through 262 removed outlier: 4.111A pdb=" N ARG C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 288 through 302 removed outlier: 3.594A pdb=" N ALA C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 346 Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 408 through 424 Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.572A pdb=" N VAL C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.724A pdb=" N GLU D 118 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 242 through 262 removed outlier: 4.173A pdb=" N ARG D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 288 through 302 Processing helix chain 'D' and resid 333 through 348 Processing helix chain 'D' and resid 350 through 364 removed outlier: 3.547A pdb=" N THR D 354 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.993A pdb=" N ARG D 388 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 430 through 439 Processing helix chain 'D' and resid 512 through 533 removed outlier: 3.568A pdb=" N VAL D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 546 Processing sheet with id=AA1, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA2, first strand: chain 'B' and resid 188 through 191 removed outlier: 6.633A pdb=" N ALA B 188 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR B 224 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU B 190 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR B 226 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 325 through 332 removed outlier: 4.146A pdb=" N GLU B 495 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL B 452 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA B 373 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE B 454 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU B 456 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.629A pdb=" N THR C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.482A pdb=" N ALA C 188 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR C 224 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU C 190 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR C 226 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 333 removed outlier: 4.174A pdb=" N GLU C 495 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL C 452 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA C 373 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE C 454 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU C 456 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AA8, first strand: chain 'D' and resid 188 through 191 removed outlier: 6.469A pdb=" N ALA D 188 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR D 224 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU D 190 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR D 226 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 325 through 332 removed outlier: 4.206A pdb=" N GLU D 495 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N VAL D 452 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA D 373 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE D 454 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU D 456 " --> pdb=" O GLY D 375 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1512 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: 1.61 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3509 1.34 - 1.46: 1915 1.46 - 1.58: 5113 1.58 - 1.69: 1 1.69 - 1.81: 42 Bond restraints: 10580 Sorted by residual: bond pdb=" CB PRO B 444 " pdb=" CG PRO B 444 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.19e+00 bond pdb=" CA PHE C 286 " pdb=" CB PHE C 286 " ideal model delta sigma weight residual 1.526 1.554 -0.028 1.76e-02 3.23e+03 2.51e+00 bond pdb=" CD1 PHE B 475 " pdb=" CE1 PHE B 475 " ideal model delta sigma weight residual 1.382 1.423 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CE1 PHE B 475 " pdb=" CZ PHE B 475 " ideal model delta sigma weight residual 1.382 1.422 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG LEU B 362 " pdb=" CD1 LEU B 362 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.22e-01 ... (remaining 10575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 14140 1.67 - 3.33: 249 3.33 - 5.00: 27 5.00 - 6.66: 4 6.66 - 8.33: 1 Bond angle restraints: 14421 Sorted by residual: angle pdb=" CA PRO B 444 " pdb=" N PRO B 444 " pdb=" CD PRO B 444 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CD1 PHE B 475 " pdb=" CE1 PHE B 475 " pdb=" CZ PHE B 475 " ideal model delta sigma weight residual 120.00 126.14 -6.14 1.80e+00 3.09e-01 1.16e+01 angle pdb=" C GLU D 118 " pdb=" N LEU D 119 " pdb=" CA LEU D 119 " ideal model delta sigma weight residual 121.54 115.31 6.23 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C ASP D 287 " pdb=" N ALA D 288 " pdb=" CA ALA D 288 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" CA TYR B 150 " pdb=" CB TYR B 150 " pdb=" CG TYR B 150 " ideal model delta sigma weight residual 113.90 118.28 -4.38 1.80e+00 3.09e-01 5.91e+00 ... (remaining 14416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5811 17.66 - 35.32: 447 35.32 - 52.98: 62 52.98 - 70.64: 18 70.64 - 88.30: 12 Dihedral angle restraints: 6350 sinusoidal: 2503 harmonic: 3847 Sorted by residual: dihedral pdb=" CA LEU C 119 " pdb=" C LEU C 119 " pdb=" N TRP C 120 " pdb=" CA TRP C 120 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ARG B 208 " pdb=" C ARG B 208 " pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta harmonic sigma weight residual 180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU D 119 " pdb=" C LEU D 119 " pdb=" N TRP D 120 " pdb=" CA TRP D 120 " ideal model delta harmonic sigma weight residual 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 981 0.028 - 0.055: 383 0.055 - 0.083: 121 0.083 - 0.111: 100 0.111 - 0.139: 20 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CG LEU C 528 " pdb=" CB LEU C 528 " pdb=" CD1 LEU C 528 " pdb=" CD2 LEU C 528 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA PHE C 286 " pdb=" N PHE C 286 " pdb=" C PHE C 286 " pdb=" CB PHE C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA PRO B 497 " pdb=" N PRO B 497 " pdb=" C PRO B 497 " pdb=" CB PRO B 497 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1602 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 443 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO B 444 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 444 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 444 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 496 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 497 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 497 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 497 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 441 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B 442 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " 0.025 5.00e-02 4.00e+02 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 184 2.70 - 3.25: 9309 3.25 - 3.80: 16068 3.80 - 4.35: 21190 4.35 - 4.90: 35361 Nonbonded interactions: 82112 Sorted by model distance: nonbonded pdb=" O THR B 183 " pdb=" NH1 ARG B 215 " model vdw 2.151 3.120 nonbonded pdb=" NE2 GLN D 295 " pdb=" OD2 ASP D 437 " model vdw 2.214 3.120 nonbonded pdb=" NH1 ARG B 525 " pdb=" O ALA B 545 " model vdw 2.217 3.120 nonbonded pdb=" OD1 ASP D 181 " pdb=" NH2 ARG D 215 " model vdw 2.237 3.120 nonbonded pdb=" NH2 ARG B 299 " pdb=" OD2 ASP B 437 " model vdw 2.257 3.120 ... (remaining 82107 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 'B' and (resid 101 through 117 or (resid 118 and (name N or name CA or na \ me C or name O )) or resid 119 through 292 or (resid 293 and (name N or name CA \ or name C or name O or name CB )) or resid 294 through 303 or (resid 304 and (na \ me N or name CA or name C or name O or name CB )) or resid 305 through 367 or (r \ esid 368 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 369 or (resid 370 through 371 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or resid 372 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 460 or ( \ resid 471 and (name C or name O )) or resid 472 through 539 or (resid 540 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ )) or resid 541 through 542 or (resid 543 and (name N or name CA or name C or n \ ame O or name CB or name CG )) or (resid 544 through 547 and (name N or name CA \ or name C or name O or name CB )) or (resid 548 and (name N )))) selection = (chain 'C' and (resid 101 through 264 or (resid 265 and (name N or name CA or na \ me C or name O or name CB )) or resid 266 through 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 386 through 459 \ or (resid 460 and (name N or name CA )) or resid 471 through 474 or (resid 475 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CE1 or name CE2 or name CZ )) or resid 476 through 548)) selection = (chain 'D' and (resid 101 through 117 or (resid 118 and (name N or name CA or na \ me C or name O )) or resid 119 through 264 or (resid 265 and (name N or name CA \ or name C or name O or name CB )) or resid 266 through 292 or (resid 293 and (na \ me N or name CA or name C or name O or name CB )) or resid 294 through 303 or (r \ esid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 t \ hrough 367 or (resid 368 and (name N or name CA or name C or name O or name CB o \ r name CG )) or resid 369 or (resid 370 through 371 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD )) or resid 372 through 384 or ( \ resid 385 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 386 through 432 or (resid 433 and (name N or name CA or name C or name O \ or name CB )) or resid 434 through 459 or (resid 460 and (name N or name CA )) o \ r (resid 471 and (name C or name O )) or resid 472 through 474 or (resid 475 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CE1 or name CE2 or name CZ )) or resid 476 through 539 or (resid 540 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE )) \ or resid 541 through 542 or (resid 543 and (name N or name CA or name C or name \ O or name CB or name CG )) or (resid 544 through 547 and (name N or name CA or \ name C or name O or name CB )) or (resid 548 and (name N )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.950 Find NCS groups from input model: 0.220 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 0.089 10580 Z= 0.114 Angle : 0.531 8.331 14421 Z= 0.285 Chirality : 0.040 0.139 1605 Planarity : 0.005 0.102 1906 Dihedral : 13.276 88.302 3874 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.63 (0.23), residues: 1312 helix: 1.64 (0.23), residues: 499 sheet: 0.53 (0.28), residues: 313 loop : -0.90 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 501 TYR 0.030 0.001 TYR B 150 PHE 0.020 0.002 PHE D 241 TRP 0.015 0.001 TRP D 120 HIS 0.003 0.000 HIS D 230 Details of bonding type rmsd covalent geometry : bond 0.00262 (10580) covalent geometry : angle 0.53060 (14421) hydrogen bonds : bond 0.16663 ( 528) hydrogen bonds : angle 5.89218 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.393 Fit side-chains REVERT: B 295 GLN cc_start: 0.6989 (mt0) cc_final: 0.6760 (mt0) REVERT: B 436 ARG cc_start: 0.5734 (mtm-85) cc_final: 0.5362 (ptp90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.8492 time to fit residues: 125.0109 Evaluate side-chains 117 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 HIS B 282 GLN C 258 GLN D 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.175297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122546 restraints weight = 10166.495| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.10 r_work: 0.3207 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10580 Z= 0.125 Angle : 0.535 6.166 14421 Z= 0.283 Chirality : 0.041 0.137 1605 Planarity : 0.005 0.061 1906 Dihedral : 4.163 17.947 1488 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.43 % Favored : 96.42 % Rotamer: Outliers : 0.84 % Allowed : 6.18 % Favored : 92.98 % 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 aren not related in a simple way. whole: 0.95 (0.23), residues: 1312 helix: 2.06 (0.23), residues: 502 sheet: 0.71 (0.28), residues: 308 loop : -0.91 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 501 TYR 0.023 0.001 TYR C 150 PHE 0.020 0.002 PHE D 241 TRP 0.012 0.001 TRP B 120 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00285 (10580) covalent geometry : angle 0.53498 (14421) hydrogen bonds : bond 0.04556 ( 528) hydrogen bonds : angle 4.44484 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.432 Fit side-chains REVERT: B 142 ILE cc_start: 0.8674 (mt) cc_final: 0.8364 (mp) REVERT: B 312 ARG cc_start: 0.6608 (mtm-85) cc_final: 0.6279 (mtm-85) REVERT: B 329 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 387 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: B 436 ARG cc_start: 0.5888 (mtm-85) cc_final: 0.5457 (ptt90) REVERT: C 137 MET cc_start: 0.8466 (ttm) cc_final: 0.8143 (ttm) REVERT: C 339 GLN cc_start: 0.7191 (mm110) cc_final: 0.6986 (mt0) REVERT: C 344 SER cc_start: 0.7473 (m) cc_final: 0.7185 (p) REVERT: C 411 ASP cc_start: 0.8043 (m-30) cc_final: 0.7803 (m-30) REVERT: D 203 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8237 (ttt-90) REVERT: D 273 VAL cc_start: 0.8010 (m) cc_final: 0.7777 (p) REVERT: D 387 GLU cc_start: 0.7151 (tp30) cc_final: 0.6289 (tt0) outliers start: 9 outliers final: 1 residues processed: 126 average time/residue: 0.9370 time to fit residues: 124.1839 Evaluate side-chains 115 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 307 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 124 optimal weight: 0.0030 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.178222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135579 restraints weight = 10279.075| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.94 r_work: 0.3216 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10580 Z= 0.092 Angle : 0.472 6.229 14421 Z= 0.247 Chirality : 0.040 0.130 1605 Planarity : 0.004 0.054 1906 Dihedral : 3.842 19.254 1488 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 1.12 % Allowed : 7.49 % Favored : 91.39 % 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 aren not related in a simple way. whole: 1.23 (0.23), residues: 1312 helix: 2.42 (0.23), residues: 496 sheet: 0.67 (0.28), residues: 312 loop : -0.74 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 501 TYR 0.010 0.001 TYR B 168 PHE 0.015 0.001 PHE C 249 TRP 0.012 0.001 TRP D 120 HIS 0.002 0.000 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00202 (10580) covalent geometry : angle 0.47206 (14421) hydrogen bonds : bond 0.03574 ( 528) hydrogen bonds : angle 4.13681 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.344 Fit side-chains REVERT: B 142 ILE cc_start: 0.8663 (mt) cc_final: 0.8343 (mp) REVERT: B 329 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6834 (tm-30) REVERT: B 387 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: B 436 ARG cc_start: 0.5866 (mtm-85) cc_final: 0.5459 (ptt90) REVERT: C 283 ARG cc_start: 0.8072 (ttp-170) cc_final: 0.7629 (ttp-170) REVERT: C 344 SER cc_start: 0.7481 (m) cc_final: 0.7085 (p) REVERT: C 387 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7637 (tt0) REVERT: C 411 ASP cc_start: 0.8092 (m-30) cc_final: 0.7859 (m-30) REVERT: D 118 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6511 (tt0) REVERT: D 273 VAL cc_start: 0.8023 (m) cc_final: 0.7816 (p) REVERT: D 387 GLU cc_start: 0.7182 (tp30) cc_final: 0.6202 (tt0) REVERT: D 525 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7529 (mmm160) outliers start: 12 outliers final: 4 residues processed: 131 average time/residue: 0.8656 time to fit residues: 119.5694 Evaluate side-chains 120 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 307 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN D 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.175517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122909 restraints weight = 10260.513| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.11 r_work: 0.3206 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10580 Z= 0.114 Angle : 0.502 6.291 14421 Z= 0.263 Chirality : 0.040 0.131 1605 Planarity : 0.004 0.054 1906 Dihedral : 3.893 17.490 1488 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.82 % Favored : 97.03 % Rotamer: Outliers : 1.40 % Allowed : 8.52 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.23), residues: 1312 helix: 2.36 (0.23), residues: 503 sheet: 0.62 (0.28), residues: 312 loop : -0.76 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 501 TYR 0.010 0.001 TYR D 297 PHE 0.020 0.002 PHE D 241 TRP 0.011 0.001 TRP D 120 HIS 0.003 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00261 (10580) covalent geometry : angle 0.50198 (14421) hydrogen bonds : bond 0.04037 ( 528) hydrogen bonds : angle 4.14314 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.405 Fit side-chains REVERT: B 142 ILE cc_start: 0.8672 (mt) cc_final: 0.8341 (mp) REVERT: B 312 ARG cc_start: 0.6573 (mtm-85) cc_final: 0.6323 (mtm-85) REVERT: B 329 GLU cc_start: 0.7329 (tm-30) cc_final: 0.7128 (tm-30) REVERT: B 387 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: B 436 ARG cc_start: 0.5857 (mtm-85) cc_final: 0.5449 (ptt90) REVERT: B 495 GLU cc_start: 0.8186 (tt0) cc_final: 0.7744 (mt-10) REVERT: C 283 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: C 344 SER cc_start: 0.7496 (m) cc_final: 0.7080 (p) REVERT: C 411 ASP cc_start: 0.8080 (m-30) cc_final: 0.7858 (m-30) REVERT: D 118 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6648 (tt0) REVERT: D 203 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8018 (ttt-90) REVERT: D 273 VAL cc_start: 0.8071 (m) cc_final: 0.7865 (p) REVERT: D 387 GLU cc_start: 0.7218 (tp30) cc_final: 0.6196 (tt0) REVERT: D 406 GLU cc_start: 0.7795 (mp0) cc_final: 0.7525 (pm20) REVERT: D 525 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7510 (mmm160) outliers start: 15 outliers final: 7 residues processed: 126 average time/residue: 0.9131 time to fit residues: 121.0787 Evaluate side-chains 123 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN D 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.171662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121674 restraints weight = 10231.029| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.43 r_work: 0.3150 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10580 Z= 0.174 Angle : 0.576 6.612 14421 Z= 0.303 Chirality : 0.043 0.147 1605 Planarity : 0.005 0.053 1906 Dihedral : 4.275 17.740 1488 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.58 % Favored : 96.27 % Rotamer: Outliers : 1.87 % Allowed : 8.33 % Favored : 89.79 % 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 aren not related in a simple way. whole: 0.99 (0.23), residues: 1312 helix: 2.23 (0.23), residues: 497 sheet: 0.51 (0.28), residues: 312 loop : -0.86 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 501 TYR 0.012 0.002 TYR C 168 PHE 0.027 0.003 PHE D 241 TRP 0.012 0.002 TRP B 120 HIS 0.004 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00420 (10580) covalent geometry : angle 0.57640 (14421) hydrogen bonds : bond 0.05054 ( 528) hydrogen bonds : angle 4.34053 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.432 Fit side-chains REVERT: B 142 ILE cc_start: 0.8676 (mt) cc_final: 0.8377 (mp) REVERT: B 200 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: B 329 GLU cc_start: 0.7243 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 387 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: B 436 ARG cc_start: 0.6225 (mtm-85) cc_final: 0.5717 (ptt90) REVERT: B 495 GLU cc_start: 0.8232 (tt0) cc_final: 0.7761 (mt-10) REVERT: C 283 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7569 (ttp-170) REVERT: C 344 SER cc_start: 0.7613 (m) cc_final: 0.7173 (p) REVERT: C 411 ASP cc_start: 0.8096 (m-30) cc_final: 0.7874 (m-30) REVERT: C 417 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.6977 (tp40) REVERT: D 203 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8105 (ttt-90) REVERT: D 293 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7433 (mtt-85) REVERT: D 387 GLU cc_start: 0.7351 (tp30) cc_final: 0.6295 (tt0) REVERT: D 406 GLU cc_start: 0.7852 (mp0) cc_final: 0.7587 (pm20) outliers start: 20 outliers final: 9 residues processed: 128 average time/residue: 0.8665 time to fit residues: 117.1215 Evaluate side-chains 126 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 129 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN C 254 ASN C 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125735 restraints weight = 10277.279| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.31 r_work: 0.3177 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10580 Z= 0.141 Angle : 0.536 6.321 14421 Z= 0.281 Chirality : 0.042 0.139 1605 Planarity : 0.005 0.054 1906 Dihedral : 4.165 17.424 1488 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 1.87 % Allowed : 9.27 % Favored : 88.86 % 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 aren not related in a simple way. whole: 1.02 (0.23), residues: 1312 helix: 2.26 (0.23), residues: 497 sheet: 0.54 (0.28), residues: 313 loop : -0.87 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 501 TYR 0.011 0.002 TYR D 297 PHE 0.023 0.002 PHE D 241 TRP 0.011 0.001 TRP B 120 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00334 (10580) covalent geometry : angle 0.53552 (14421) hydrogen bonds : bond 0.04468 ( 528) hydrogen bonds : angle 4.21653 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.414 Fit side-chains REVERT: B 142 ILE cc_start: 0.8685 (mt) cc_final: 0.8366 (mp) REVERT: B 329 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: B 387 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: B 436 ARG cc_start: 0.6294 (mtm-85) cc_final: 0.5811 (ptt90) REVERT: B 495 GLU cc_start: 0.8160 (tt0) cc_final: 0.7706 (mt-10) REVERT: C 283 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7542 (ttp-170) REVERT: C 344 SER cc_start: 0.7636 (m) cc_final: 0.7202 (p) REVERT: C 387 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: C 411 ASP cc_start: 0.8078 (m-30) cc_final: 0.7850 (m-30) REVERT: C 417 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.6828 (tp40) REVERT: C 529 LYS cc_start: 0.6918 (mptt) cc_final: 0.6503 (tppt) REVERT: D 203 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8022 (ttt-90) REVERT: D 273 VAL cc_start: 0.8099 (m) cc_final: 0.7886 (p) REVERT: D 293 ARG cc_start: 0.7642 (mtt90) cc_final: 0.7384 (mtt-85) REVERT: D 387 GLU cc_start: 0.7259 (tp30) cc_final: 0.6213 (tt0) REVERT: D 406 GLU cc_start: 0.7830 (mp0) cc_final: 0.7593 (pm20) outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 0.8627 time to fit residues: 115.5121 Evaluate side-chains 127 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.171841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124401 restraints weight = 10178.540| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.09 r_work: 0.3168 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10580 Z= 0.142 Angle : 0.539 6.245 14421 Z= 0.283 Chirality : 0.042 0.141 1605 Planarity : 0.005 0.054 1906 Dihedral : 4.163 17.228 1488 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.28 % Favored : 96.57 % Rotamer: Outliers : 2.25 % Allowed : 9.74 % Favored : 88.01 % 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 aren not related in a simple way. whole: 1.06 (0.23), residues: 1312 helix: 2.29 (0.23), residues: 498 sheet: 0.54 (0.28), residues: 313 loop : -0.83 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 494 TYR 0.011 0.002 TYR C 168 PHE 0.024 0.002 PHE D 241 TRP 0.012 0.002 TRP B 120 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00336 (10580) covalent geometry : angle 0.53917 (14421) hydrogen bonds : bond 0.04561 ( 528) hydrogen bonds : angle 4.21688 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.510 Fit side-chains REVERT: B 142 ILE cc_start: 0.8689 (mt) cc_final: 0.8376 (mp) REVERT: B 329 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: B 387 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: B 436 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.5903 (ptt90) REVERT: B 495 GLU cc_start: 0.8193 (tt0) cc_final: 0.7725 (mt-10) REVERT: B 547 ASP cc_start: 0.6444 (m-30) cc_final: 0.6224 (m-30) REVERT: C 270 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: C 283 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7550 (ttp-170) REVERT: C 344 SER cc_start: 0.7678 (m) cc_final: 0.7226 (p) REVERT: C 411 ASP cc_start: 0.8120 (m-30) cc_final: 0.7892 (m-30) REVERT: C 417 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6920 (tp40) REVERT: C 529 LYS cc_start: 0.6850 (mptt) cc_final: 0.6477 (tppt) REVERT: D 203 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8026 (ttt-90) REVERT: D 273 VAL cc_start: 0.8137 (m) cc_final: 0.7931 (p) REVERT: D 293 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7403 (mtt-85) REVERT: D 387 GLU cc_start: 0.7303 (tp30) cc_final: 0.6268 (tt0) REVERT: D 406 GLU cc_start: 0.7865 (mp0) cc_final: 0.7613 (pm20) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 0.8450 time to fit residues: 114.1375 Evaluate side-chains 134 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 37 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 127 HIS C 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.173106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121208 restraints weight = 10181.850| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.04 r_work: 0.3184 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10580 Z= 0.130 Angle : 0.528 6.300 14421 Z= 0.277 Chirality : 0.042 0.135 1605 Planarity : 0.005 0.056 1906 Dihedral : 4.098 17.592 1488 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.90 % Favored : 96.95 % Rotamer: Outliers : 2.25 % Allowed : 10.11 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.23), residues: 1312 helix: 2.35 (0.23), residues: 498 sheet: 0.58 (0.28), residues: 313 loop : -0.81 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 494 TYR 0.011 0.001 TYR D 297 PHE 0.022 0.002 PHE D 241 TRP 0.012 0.001 TRP D 120 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00305 (10580) covalent geometry : angle 0.52848 (14421) hydrogen bonds : bond 0.04336 ( 528) hydrogen bonds : angle 4.16396 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.426 Fit side-chains REVERT: B 142 ILE cc_start: 0.8716 (mt) cc_final: 0.8400 (mp) REVERT: B 200 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6808 (tt0) REVERT: B 387 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: B 436 ARG cc_start: 0.6318 (mtm-85) cc_final: 0.5869 (ptt90) REVERT: B 495 GLU cc_start: 0.8135 (tt0) cc_final: 0.7685 (mt-10) REVERT: C 270 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: C 283 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7503 (ttp-170) REVERT: C 344 SER cc_start: 0.7678 (m) cc_final: 0.7282 (p) REVERT: C 411 ASP cc_start: 0.8074 (m-30) cc_final: 0.7829 (m-30) REVERT: C 417 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6825 (tp40) REVERT: C 529 LYS cc_start: 0.6891 (mptt) cc_final: 0.6477 (tppt) REVERT: D 203 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7964 (ttt-90) REVERT: D 293 ARG cc_start: 0.7582 (mtt90) cc_final: 0.7350 (mtt-85) REVERT: D 387 GLU cc_start: 0.7214 (tp30) cc_final: 0.6165 (tt0) REVERT: D 406 GLU cc_start: 0.7806 (mp0) cc_final: 0.7569 (pm20) outliers start: 24 outliers final: 13 residues processed: 129 average time/residue: 0.8287 time to fit residues: 112.8962 Evaluate side-chains 128 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.173571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125674 restraints weight = 10137.959| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.21 r_work: 0.3204 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10580 Z= 0.118 Angle : 0.513 6.260 14421 Z= 0.269 Chirality : 0.041 0.130 1605 Planarity : 0.005 0.056 1906 Dihedral : 4.027 17.972 1488 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 2.15 % Allowed : 10.21 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.24), residues: 1312 helix: 2.34 (0.23), residues: 503 sheet: 0.60 (0.28), residues: 313 loop : -0.80 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 494 TYR 0.010 0.001 TYR D 297 PHE 0.021 0.002 PHE D 241 TRP 0.012 0.001 TRP D 120 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00274 (10580) covalent geometry : angle 0.51306 (14421) hydrogen bonds : bond 0.04108 ( 528) hydrogen bonds : angle 4.11334 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.396 Fit side-chains REVERT: B 142 ILE cc_start: 0.8699 (mt) cc_final: 0.8389 (mp) REVERT: B 200 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6776 (tt0) REVERT: B 215 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6569 (ttt-90) REVERT: B 387 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: B 436 ARG cc_start: 0.6302 (mtm-85) cc_final: 0.5849 (ptt90) REVERT: C 270 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: C 283 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7503 (ttp-170) REVERT: C 344 SER cc_start: 0.7643 (m) cc_final: 0.7234 (p) REVERT: C 411 ASP cc_start: 0.8069 (m-30) cc_final: 0.7842 (m-30) REVERT: C 417 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6820 (tp40) REVERT: C 529 LYS cc_start: 0.6795 (mptt) cc_final: 0.6389 (tppt) REVERT: D 203 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7953 (ttt-90) REVERT: D 293 ARG cc_start: 0.7528 (mtt90) cc_final: 0.7282 (mtt-85) REVERT: D 387 GLU cc_start: 0.7187 (tp30) cc_final: 0.6120 (tt0) REVERT: D 406 GLU cc_start: 0.7790 (mp0) cc_final: 0.7553 (pm20) outliers start: 23 outliers final: 13 residues processed: 127 average time/residue: 0.8327 time to fit residues: 111.5116 Evaluate side-chains 128 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129242 restraints weight = 10026.660| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.96 r_work: 0.3131 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10580 Z= 0.145 Angle : 0.547 6.186 14421 Z= 0.287 Chirality : 0.042 0.143 1605 Planarity : 0.005 0.055 1906 Dihedral : 4.172 17.723 1488 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.35 % Favored : 96.49 % Rotamer: Outliers : 2.15 % Allowed : 10.39 % Favored : 87.45 % 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 aren not related in a simple way. whole: 1.12 (0.23), residues: 1312 helix: 2.35 (0.23), residues: 497 sheet: 0.57 (0.28), residues: 313 loop : -0.80 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 494 TYR 0.011 0.002 TYR C 168 PHE 0.024 0.002 PHE D 241 TRP 0.010 0.001 TRP D 120 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00344 (10580) covalent geometry : angle 0.54695 (14421) hydrogen bonds : bond 0.04612 ( 528) hydrogen bonds : angle 4.21911 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.483 Fit side-chains REVERT: B 142 ILE cc_start: 0.8659 (mt) cc_final: 0.8351 (mp) REVERT: B 200 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6807 (tt0) REVERT: B 215 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6520 (ttt-90) REVERT: B 387 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: B 436 ARG cc_start: 0.6386 (mtm-85) cc_final: 0.5883 (ptt90) REVERT: B 495 GLU cc_start: 0.7999 (tt0) cc_final: 0.7794 (mt-10) REVERT: C 270 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: C 283 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7499 (ttp-170) REVERT: C 344 SER cc_start: 0.7714 (m) cc_final: 0.7309 (p) REVERT: C 411 ASP cc_start: 0.8116 (m-30) cc_final: 0.7896 (m-30) REVERT: C 417 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.6903 (tp40) REVERT: C 529 LYS cc_start: 0.6829 (mptt) cc_final: 0.6453 (tppt) REVERT: D 203 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8067 (ttt-90) REVERT: D 293 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7370 (mtt-85) REVERT: D 387 GLU cc_start: 0.7345 (tp30) cc_final: 0.6251 (tt0) REVERT: D 406 GLU cc_start: 0.7872 (mp0) cc_final: 0.7572 (pm20) outliers start: 23 outliers final: 15 residues processed: 126 average time/residue: 0.8798 time to fit residues: 117.0158 Evaluate side-chains 131 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.172992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126082 restraints weight = 10202.821| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.28 r_work: 0.3192 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10580 Z= 0.131 Angle : 0.525 6.334 14421 Z= 0.275 Chirality : 0.042 0.136 1605 Planarity : 0.005 0.055 1906 Dihedral : 4.072 18.213 1488 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.90 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 10.49 % Favored : 87.45 % 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 aren not related in a simple way. whole: 1.17 (0.23), residues: 1312 helix: 2.39 (0.23), residues: 497 sheet: 0.60 (0.28), residues: 313 loop : -0.77 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 494 TYR 0.010 0.001 TYR D 297 PHE 0.022 0.002 PHE D 241 TRP 0.012 0.001 TRP D 120 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00308 (10580) covalent geometry : angle 0.52528 (14421) hydrogen bonds : bond 0.04268 ( 528) hydrogen bonds : angle 4.13419 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4749.48 seconds wall clock time: 81 minutes 27.57 seconds (4887.57 seconds total)