Starting phenix.real_space_refine on Mon Jun 9 06:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0s_39714/06_2025/8z0s_39714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0s_39714/06_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_39714/06_2025/8z0s_39714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0s_39714/06_2025/8z0s_39714.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0s_39714/06_2025/8z0s_39714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0s_39714/06_2025/8z0s_39714.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ARG:plan': 3, 'ASP:plan': 6} 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: 6.92, per 1000 atoms: 0.67 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.04 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: 3.52 Time building geometry restraints manager: 2.87 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: 1.450 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.840 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP D 120 HIS 0.003 0.000 HIS D 230 PHE 0.020 0.002 PHE D 241 TYR 0.030 0.001 TYR B 150 ARG 0.004 0.000 ARG D 501 Details of bonding type rmsd hydrogen bonds : bond 0.16663 ( 528) hydrogen bonds : angle 5.89218 ( 1512) covalent geometry : bond 0.00262 (10580) covalent geometry : angle 0.53060 (14421) *********************** 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 : 1.072 Fit side-chains REVERT: B 295 GLN cc_start: 0.6989 (mt0) cc_final: 0.6754 (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: 1.6763 time to fit residues: 247.8951 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 : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 76 optimal weight: 0.0000 chunk 118 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.176861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124448 restraints weight = 10097.467| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.09 r_work: 0.3231 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10580 Z= 0.107 Angle : 0.510 6.214 14421 Z= 0.270 Chirality : 0.040 0.130 1605 Planarity : 0.005 0.061 1906 Dihedral : 4.045 18.530 1488 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 0.66 % Allowed : 5.90 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1312 helix: 2.12 (0.23), residues: 502 sheet: 0.73 (0.28), residues: 310 loop : -0.85 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 120 HIS 0.004 0.000 HIS C 280 PHE 0.017 0.002 PHE D 241 TYR 0.021 0.001 TYR C 150 ARG 0.005 0.000 ARG D 501 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 528) hydrogen bonds : angle 4.39460 ( 1512) covalent geometry : bond 0.00239 (10580) covalent geometry : angle 0.51025 (14421) *********************** 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 128 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 1.029 Fit side-chains REVERT: B 142 ILE cc_start: 0.8687 (mt) cc_final: 0.8371 (mp) REVERT: B 387 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: B 436 ARG cc_start: 0.5873 (mtm-85) cc_final: 0.5450 (ptt90) REVERT: C 137 MET cc_start: 0.8442 (ttm) cc_final: 0.8177 (ttm) REVERT: C 339 GLN cc_start: 0.7196 (mm110) cc_final: 0.6992 (mt0) REVERT: C 344 SER cc_start: 0.7447 (m) cc_final: 0.7151 (p) REVERT: C 411 ASP cc_start: 0.8014 (m-30) cc_final: 0.7765 (m-30) REVERT: D 273 VAL cc_start: 0.7975 (m) cc_final: 0.7751 (p) REVERT: D 387 GLU cc_start: 0.7183 (tp30) cc_final: 0.6326 (tt0) outliers start: 7 outliers final: 1 residues processed: 125 average time/residue: 1.8253 time to fit residues: 240.6874 Evaluate side-chains 113 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 88 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 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 = 0.3911 r_free = 0.3911 target = 0.172638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119951 restraints weight = 10235.996| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.10 r_work: 0.3166 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1243 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= 0.169 Angle : 0.579 6.252 14421 Z= 0.304 Chirality : 0.043 0.143 1605 Planarity : 0.005 0.055 1906 Dihedral : 4.323 17.111 1488 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.28 % Favored : 96.49 % Rotamer: Outliers : 1.59 % Allowed : 7.40 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1312 helix: 2.10 (0.23), residues: 498 sheet: 0.57 (0.28), residues: 310 loop : -0.91 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 120 HIS 0.004 0.001 HIS C 280 PHE 0.026 0.003 PHE D 241 TYR 0.024 0.002 TYR C 150 ARG 0.005 0.000 ARG D 501 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 528) hydrogen bonds : angle 4.42660 ( 1512) covalent geometry : bond 0.00409 (10580) covalent geometry : angle 0.57905 (14421) *********************** 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 131 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.277 Fit side-chains REVERT: B 142 ILE cc_start: 0.8689 (mt) cc_final: 0.8373 (mp) REVERT: B 200 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: B 312 ARG cc_start: 0.6659 (mtm-85) cc_final: 0.6374 (mtm-85) REVERT: B 387 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: B 436 ARG cc_start: 0.5987 (mtm-85) cc_final: 0.5599 (ptt90) REVERT: C 283 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7615 (ttp-170) REVERT: C 344 SER cc_start: 0.7630 (m) cc_final: 0.7177 (p) REVERT: C 411 ASP cc_start: 0.8052 (m-30) cc_final: 0.7823 (m-30) REVERT: D 203 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8054 (ttt-90) REVERT: D 387 GLU cc_start: 0.7330 (tp30) cc_final: 0.6331 (tt0) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 2.0904 time to fit residues: 271.8678 Evaluate side-chains 122 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 B residue 394 ILE Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 362 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 389 LEU Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 14 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 103 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.176374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128692 restraints weight = 10150.186| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.23 r_work: 0.3237 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1435 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= 0.096 Angle : 0.484 6.310 14421 Z= 0.253 Chirality : 0.040 0.129 1605 Planarity : 0.004 0.055 1906 Dihedral : 3.928 19.191 1488 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.33 % Rotamer: Outliers : 1.50 % Allowed : 8.15 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1312 helix: 2.32 (0.23), residues: 502 sheet: 0.62 (0.28), residues: 312 loop : -0.81 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 120 HIS 0.002 0.000 HIS C 280 PHE 0.016 0.002 PHE D 241 TYR 0.010 0.001 TYR B 275 ARG 0.004 0.000 ARG D 501 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 528) hydrogen bonds : angle 4.13194 ( 1512) covalent geometry : bond 0.00212 (10580) covalent geometry : angle 0.48358 (14421) *********************** 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 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: B 116 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.5393 (mp10) REVERT: B 142 ILE cc_start: 0.8658 (mt) cc_final: 0.8336 (mp) REVERT: B 200 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6701 (tt0) REVERT: B 312 ARG cc_start: 0.6592 (mtm-85) cc_final: 0.6336 (mtm-85) REVERT: B 387 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: B 436 ARG cc_start: 0.6141 (mtm-85) cc_final: 0.5733 (ptt90) REVERT: B 495 GLU cc_start: 0.8152 (tt0) cc_final: 0.7634 (mt-10) REVERT: C 283 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.7498 (ttp-170) REVERT: C 344 SER cc_start: 0.7460 (m) cc_final: 0.7066 (p) REVERT: C 387 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7752 (mp0) REVERT: C 411 ASP cc_start: 0.8031 (m-30) cc_final: 0.7784 (m-30) REVERT: D 203 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7974 (ttt-90) REVERT: D 387 GLU cc_start: 0.7099 (tp30) cc_final: 0.6069 (tt0) REVERT: D 525 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7429 (mmm160) outliers start: 16 outliers final: 5 residues processed: 134 average time/residue: 1.7901 time to fit residues: 253.2587 Evaluate side-chains 120 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 200 GLU 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 362 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 307 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN D 254 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.175420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132741 restraints weight = 10121.973| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.21 r_work: 0.3164 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10580 Z= 0.107 Angle : 0.498 6.795 14421 Z= 0.260 Chirality : 0.040 0.129 1605 Planarity : 0.004 0.054 1906 Dihedral : 3.903 18.149 1488 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.67 % Favored : 97.18 % Rotamer: Outliers : 1.40 % Allowed : 8.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1312 helix: 2.35 (0.23), residues: 503 sheet: 0.63 (0.28), residues: 312 loop : -0.78 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 120 HIS 0.002 0.001 HIS D 221 PHE 0.019 0.002 PHE D 241 TYR 0.011 0.001 TYR C 150 ARG 0.004 0.000 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 528) hydrogen bonds : angle 4.10700 ( 1512) covalent geometry : bond 0.00243 (10580) covalent geometry : angle 0.49811 (14421) *********************** 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 132 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: B 116 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.5509 (mp10) REVERT: B 142 ILE cc_start: 0.8735 (mt) cc_final: 0.8414 (mp) REVERT: B 200 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: B 312 ARG cc_start: 0.6611 (mtm-85) cc_final: 0.6335 (mtm-85) REVERT: B 329 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 387 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: B 436 ARG cc_start: 0.6153 (mtm-85) cc_final: 0.5768 (ptt90) REVERT: B 495 GLU cc_start: 0.8199 (tt0) cc_final: 0.7882 (mt-10) REVERT: C 270 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: C 344 SER cc_start: 0.7533 (m) cc_final: 0.7116 (p) REVERT: C 411 ASP cc_start: 0.8148 (m-30) cc_final: 0.7928 (m-30) REVERT: C 529 LYS cc_start: 0.6915 (mptt) cc_final: 0.6495 (tppt) REVERT: D 203 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8101 (ttt-90) REVERT: D 293 ARG cc_start: 0.7627 (mtt180) cc_final: 0.7383 (mtt-85) REVERT: D 387 GLU cc_start: 0.7254 (tp30) cc_final: 0.6183 (tt0) REVERT: D 525 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7594 (mmm160) outliers start: 15 outliers final: 7 residues processed: 126 average time/residue: 1.7270 time to fit residues: 229.5292 Evaluate side-chains 127 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 GLN 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 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 270 GLU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 307 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 122 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.173974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126492 restraints weight = 10172.235| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.31 r_work: 0.3196 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10580 Z= 0.129 Angle : 0.526 7.057 14421 Z= 0.275 Chirality : 0.041 0.136 1605 Planarity : 0.005 0.053 1906 Dihedral : 4.047 17.360 1488 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.97 % Allowed : 8.99 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1312 helix: 2.27 (0.23), residues: 504 sheet: 0.59 (0.28), residues: 312 loop : -0.82 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 120 HIS 0.003 0.001 HIS C 280 PHE 0.022 0.002 PHE D 241 TYR 0.012 0.001 TYR C 150 ARG 0.003 0.000 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 528) hydrogen bonds : angle 4.17170 ( 1512) covalent geometry : bond 0.00304 (10580) covalent geometry : angle 0.52607 (14421) *********************** 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 137 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.024 Fit side-chains REVERT: B 116 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.5533 (mp10) REVERT: B 142 ILE cc_start: 0.8645 (mt) cc_final: 0.8324 (mp) REVERT: B 200 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: B 387 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: B 436 ARG cc_start: 0.6218 (mtm-85) cc_final: 0.5791 (ptt90) REVERT: B 495 GLU cc_start: 0.8100 (tt0) cc_final: 0.7710 (mt-10) REVERT: C 270 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: C 283 ARG cc_start: 0.8039 (ttp-170) cc_final: 0.7597 (ttp-170) REVERT: C 344 SER cc_start: 0.7534 (m) cc_final: 0.7150 (p) REVERT: C 387 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: C 411 ASP cc_start: 0.8066 (m-30) cc_final: 0.7833 (m-30) REVERT: C 417 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.6855 (tp40) REVERT: C 529 LYS cc_start: 0.6836 (mptt) cc_final: 0.6431 (tppt) REVERT: D 203 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8020 (ttt-90) REVERT: D 293 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7308 (mtt-85) REVERT: D 387 GLU cc_start: 0.7225 (tp30) cc_final: 0.6155 (tt0) REVERT: D 406 GLU cc_start: 0.7807 (mp0) cc_final: 0.7563 (pm20) REVERT: D 525 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7419 (mmm160) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 1.7389 time to fit residues: 237.5347 Evaluate side-chains 129 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 GLN 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 270 GLU 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 C residue 528 LEU Chi-restraints excluded: chain D residue 119 LEU 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 457 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 0.0060 chunk 79 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.175949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123952 restraints weight = 10325.392| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.11 r_work: 0.3223 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1789 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= 0.093 Angle : 0.477 6.347 14421 Z= 0.248 Chirality : 0.040 0.125 1605 Planarity : 0.004 0.054 1906 Dihedral : 3.811 18.861 1488 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 1.50 % Allowed : 10.11 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1312 helix: 2.46 (0.23), residues: 503 sheet: 0.63 (0.28), residues: 315 loop : -0.70 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 120 HIS 0.002 0.000 HIS D 127 PHE 0.016 0.001 PHE D 241 TYR 0.008 0.001 TYR D 297 ARG 0.004 0.000 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 528) hydrogen bonds : angle 4.00587 ( 1512) covalent geometry : bond 0.00204 (10580) covalent geometry : angle 0.47672 (14421) *********************** 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 136 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: B 116 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.5556 (mp10) REVERT: B 142 ILE cc_start: 0.8670 (mt) cc_final: 0.8344 (mp) REVERT: B 200 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6759 (tt0) REVERT: B 314 ASP cc_start: 0.6791 (m-30) cc_final: 0.6470 (p0) REVERT: B 329 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7071 (tm-30) REVERT: B 387 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: B 436 ARG cc_start: 0.6265 (mtm-85) cc_final: 0.5820 (ptt90) REVERT: B 495 GLU cc_start: 0.8042 (tt0) cc_final: 0.7722 (mt-10) REVERT: C 283 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7571 (ttp-170) REVERT: C 344 SER cc_start: 0.7581 (m) cc_final: 0.7137 (p) REVERT: C 411 ASP cc_start: 0.8106 (m-30) cc_final: 0.7896 (m-30) REVERT: C 529 LYS cc_start: 0.6812 (mptt) cc_final: 0.6351 (tppt) REVERT: D 203 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8027 (ttt-90) REVERT: D 293 ARG cc_start: 0.7555 (mtt90) cc_final: 0.7324 (mtt-85) REVERT: D 387 GLU cc_start: 0.7146 (tp30) cc_final: 0.6025 (tt0) REVERT: D 406 GLU cc_start: 0.7766 (mp0) cc_final: 0.7548 (pm20) outliers start: 16 outliers final: 7 residues processed: 131 average time/residue: 1.7647 time to fit residues: 244.8781 Evaluate side-chains 127 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 GLN 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 362 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 0.0470 chunk 37 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.177004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134161 restraints weight = 10240.732| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.18 r_work: 0.3207 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1929 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= 0.091 Angle : 0.473 7.087 14421 Z= 0.245 Chirality : 0.039 0.127 1605 Planarity : 0.004 0.054 1906 Dihedral : 3.670 18.606 1488 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 1.69 % Allowed : 10.58 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1312 helix: 2.55 (0.23), residues: 503 sheet: 0.67 (0.28), residues: 315 loop : -0.66 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 120 HIS 0.002 0.000 HIS D 127 PHE 0.016 0.001 PHE D 241 TYR 0.008 0.001 TYR D 257 ARG 0.004 0.000 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 528) hydrogen bonds : angle 3.92641 ( 1512) covalent geometry : bond 0.00200 (10580) covalent geometry : angle 0.47276 (14421) *********************** 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 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.195 Fit side-chains REVERT: B 116 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.5566 (mp10) REVERT: B 142 ILE cc_start: 0.8684 (mt) cc_final: 0.8356 (mp) REVERT: B 200 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: B 436 ARG cc_start: 0.6372 (mtm-85) cc_final: 0.5844 (ptt90) REVERT: B 495 GLU cc_start: 0.8024 (tt0) cc_final: 0.7784 (mt-10) REVERT: B 547 ASP cc_start: 0.6389 (m-30) cc_final: 0.6158 (m-30) REVERT: C 270 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: C 344 SER cc_start: 0.7606 (m) cc_final: 0.7162 (p) REVERT: C 529 LYS cc_start: 0.6812 (mptt) cc_final: 0.6335 (tppt) REVERT: D 203 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8040 (ttt-90) REVERT: D 293 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7391 (mtt-85) REVERT: D 387 GLU cc_start: 0.7173 (tp30) cc_final: 0.6029 (tm-30) REVERT: D 406 GLU cc_start: 0.7727 (mp0) cc_final: 0.7490 (pm20) REVERT: D 525 ARG cc_start: 0.8125 (mtm110) cc_final: 0.7570 (mmm160) outliers start: 18 outliers final: 10 residues processed: 133 average time/residue: 1.6401 time to fit residues: 230.8435 Evaluate side-chains 130 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 GLN 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 C residue 119 LEU Chi-restraints excluded: chain C residue 139 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 528 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS C 407 GLN D 254 ASN D 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.176106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132889 restraints weight = 10192.505| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.93 r_work: 0.3193 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1949 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= 0.098 Angle : 0.485 6.734 14421 Z= 0.253 Chirality : 0.040 0.135 1605 Planarity : 0.004 0.055 1906 Dihedral : 3.705 18.280 1488 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.10 % Rotamer: Outliers : 1.40 % Allowed : 11.24 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1312 helix: 2.56 (0.23), residues: 503 sheet: 0.68 (0.28), residues: 315 loop : -0.65 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 120 HIS 0.003 0.001 HIS C 127 PHE 0.018 0.002 PHE D 241 TYR 0.009 0.001 TYR D 297 ARG 0.004 0.000 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 528) hydrogen bonds : angle 3.94869 ( 1512) covalent geometry : bond 0.00220 (10580) covalent geometry : angle 0.48527 (14421) *********************** 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 134 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.151 Fit side-chains REVERT: B 142 ILE cc_start: 0.8691 (mt) cc_final: 0.8359 (mp) REVERT: B 200 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6743 (tt0) REVERT: B 436 ARG cc_start: 0.6255 (mtm-85) cc_final: 0.5843 (ptt90) REVERT: B 495 GLU cc_start: 0.8018 (tt0) cc_final: 0.7724 (mt-10) REVERT: C 270 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: C 283 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7599 (ttp-170) REVERT: C 344 SER cc_start: 0.7596 (m) cc_final: 0.7136 (p) REVERT: C 369 ASP cc_start: 0.8140 (m-30) cc_final: 0.7927 (m-30) REVERT: C 529 LYS cc_start: 0.6759 (mptt) cc_final: 0.6284 (tppt) REVERT: D 118 GLU cc_start: 0.6751 (tt0) cc_final: 0.6539 (tm-30) REVERT: D 203 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8024 (ttt-90) REVERT: D 293 ARG cc_start: 0.7581 (mtt90) cc_final: 0.7342 (mtt-85) REVERT: D 387 GLU cc_start: 0.7183 (tp30) cc_final: 0.6054 (tt0) REVERT: D 406 GLU cc_start: 0.7721 (mp0) cc_final: 0.7464 (pm20) REVERT: D 525 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7529 (mtp85) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 1.7680 time to fit residues: 244.0201 Evaluate side-chains 129 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 528 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 108 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS D 254 ASN D 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.176987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132282 restraints weight = 10171.204| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.28 r_work: 0.3177 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2045 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= 0.091 Angle : 0.474 6.893 14421 Z= 0.246 Chirality : 0.040 0.133 1605 Planarity : 0.004 0.055 1906 Dihedral : 3.632 18.577 1488 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 1.12 % Allowed : 11.61 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1312 helix: 2.62 (0.23), residues: 502 sheet: 0.74 (0.28), residues: 315 loop : -0.63 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 120 HIS 0.002 0.000 HIS C 127 PHE 0.016 0.001 PHE D 241 TYR 0.008 0.001 TYR D 297 ARG 0.004 0.000 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 528) hydrogen bonds : angle 3.88989 ( 1512) covalent geometry : bond 0.00203 (10580) covalent geometry : angle 0.47359 (14421) ********************** 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: 12 poor density : 122 time to evaluate : 1.051 Fit side-chains REVERT: B 142 ILE cc_start: 0.8651 (mt) cc_final: 0.8309 (mp) REVERT: B 200 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6684 (tt0) REVERT: B 217 MET cc_start: 0.7364 (mmt) cc_final: 0.7036 (mmt) REVERT: B 436 ARG cc_start: 0.6312 (mtm-85) cc_final: 0.5860 (ptt90) REVERT: B 439 VAL cc_start: 0.7384 (t) cc_final: 0.7122 (m) REVERT: B 495 GLU cc_start: 0.7864 (tt0) cc_final: 0.7621 (mt-10) REVERT: C 270 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: C 283 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7606 (ttp-170) REVERT: C 344 SER cc_start: 0.7555 (m) cc_final: 0.7111 (p) REVERT: C 529 LYS cc_start: 0.6842 (mptt) cc_final: 0.6357 (tppt) REVERT: D 203 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7899 (ttt-90) REVERT: D 293 ARG cc_start: 0.7523 (mtt90) cc_final: 0.7293 (mtt-85) REVERT: D 387 GLU cc_start: 0.7082 (tp30) cc_final: 0.6055 (tt0) REVERT: D 525 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7501 (mtp85) outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 1.6679 time to fit residues: 231.3645 Evaluate side-chains 131 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 C residue 119 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 528 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 42 optimal weight: 0.0060 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 HIS D 254 ASN D 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.175847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131732 restraints weight = 10194.480| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.08 r_work: 0.3165 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10580 Z= 0.100 Angle : 0.486 6.191 14421 Z= 0.253 Chirality : 0.040 0.132 1605 Planarity : 0.004 0.055 1906 Dihedral : 3.707 18.103 1488 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 1.22 % Allowed : 12.08 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1312 helix: 2.57 (0.23), residues: 504 sheet: 0.73 (0.28), residues: 315 loop : -0.62 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 120 HIS 0.002 0.001 HIS C 127 PHE 0.018 0.002 PHE D 241 TYR 0.009 0.001 TYR D 297 ARG 0.007 0.000 ARG C 284 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 528) hydrogen bonds : angle 3.94111 ( 1512) covalent geometry : bond 0.00226 (10580) covalent geometry : angle 0.48649 (14421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9693.85 seconds wall clock time: 168 minutes 43.55 seconds (10123.55 seconds total)