Starting phenix.real_space_refine on Thu Jul 2 21:23:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r89_24312/07_2026/7r89_24312.map" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.002 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 66 5.16 5 C 6811 2.51 5 N 1778 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10531 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4596 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 22, 'TRANS': 561} Chain breaks: 3 Chain: "B" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4202 Classifications: {'peptide': 529} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 504} Chain breaks: 5 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ERG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.24 Number of scatterers: 10531 At special positions: 0 Unit cell: (116.48, 101.504, 123.968, 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 66 16.00 O 1876 8.00 N 1778 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " distance=2.03 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: 1.03 Conformation dependent library (CDL) restraints added in 368.7 milliseconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 53.5% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.377A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 331 Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.866A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 405 removed outlier: 5.475A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.054A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.993A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 removed outlier: 3.511A pdb=" N VAL A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.638A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.241A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.658A pdb=" N PHE A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 649 Proline residue: A 632 - end of helix Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.730A pdb=" N ARG B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 228 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 459 removed outlier: 4.638A pdb=" N ILE B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 490 through 517 removed outlier: 3.844A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix removed outlier: 4.042A pdb=" N TRP B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 594 through 609 Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.804A pdb=" N MET B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.955A pdb=" N PHE C 51 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.663A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77 removed outlier: 6.624A pdb=" N LYS A 70 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER A 44 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL A 72 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE A 40 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR A 114 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N HIS A 42 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU A 112 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.354A pdb=" N MET A 214 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR A 248 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A 216 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 273 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 267 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 96 removed outlier: 5.242A pdb=" N LEU B 52 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER B 92 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG B 50 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 94 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU B 48 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 96 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 46 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 55 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 127 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 96 removed outlier: 5.242A pdb=" N LEU B 52 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER B 92 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG B 50 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 94 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU B 48 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 96 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR B 46 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.319A pdb=" N ALA B 149 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP B 237 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 151 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 101 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N MET B 100 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 284 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 102 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N MET B 286 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 104 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.133A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.348A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR D 69 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP D 55 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.348A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR D 117 " --> pdb=" O GLN D 110 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1710 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: 1.42 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3342 1.35 - 1.46: 2562 1.46 - 1.58: 4752 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 10761 Sorted by residual: bond pdb=" C10 ERG B 901 " pdb=" C9 ERG B 901 " ideal model delta sigma weight residual 1.556 1.507 0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" N ARG C 63 " pdb=" CA ARG C 63 " ideal model delta sigma weight residual 1.459 1.473 -0.015 1.16e-02 7.43e+03 1.61e+00 bond pdb=" C10 ERG B 901 " pdb=" C5 ERG B 901 " ideal model delta sigma weight residual 1.519 1.496 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.28e-02 6.10e+03 1.14e+00 ... (remaining 10756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 14277 1.58 - 3.15: 230 3.15 - 4.73: 39 4.73 - 6.30: 21 6.30 - 7.88: 4 Bond angle restraints: 14571 Sorted by residual: angle pdb=" C PRO A 556 " pdb=" N ILE A 557 " pdb=" CA ILE A 557 " ideal model delta sigma weight residual 120.33 123.30 -2.97 8.00e-01 1.56e+00 1.38e+01 angle pdb=" N VAL B 205 " pdb=" CA VAL B 205 " pdb=" CB VAL B 205 " ideal model delta sigma weight residual 112.39 108.80 3.59 1.17e+00 7.31e-01 9.42e+00 angle pdb=" C ARG C 63 " pdb=" CA ARG C 63 " pdb=" CB ARG C 63 " ideal model delta sigma weight residual 110.92 115.60 -4.68 1.59e+00 3.96e-01 8.66e+00 angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.27e+00 angle pdb=" N ILE B 459 " pdb=" CA ILE B 459 " pdb=" C ILE B 459 " ideal model delta sigma weight residual 108.88 115.05 -6.17 2.16e+00 2.14e-01 8.16e+00 ... (remaining 14566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5776 17.96 - 35.91: 446 35.91 - 53.86: 130 53.86 - 71.82: 29 71.82 - 89.77: 11 Dihedral angle restraints: 6392 sinusoidal: 2548 harmonic: 3844 Sorted by residual: dihedral pdb=" CB CYS A 587 " pdb=" SG CYS A 587 " pdb=" SG CYS A 600 " pdb=" CB CYS A 600 " ideal model delta sinusoidal sigma weight residual -86.00 -159.55 73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS D 43 " pdb=" SG CYS D 43 " pdb=" SG CYS D 108 " pdb=" CB CYS D 108 " ideal model delta sinusoidal sigma weight residual 93.00 65.05 27.95 1 1.00e+01 1.00e-02 1.12e+01 dihedral pdb=" CB GLU B 483 " pdb=" CG GLU B 483 " pdb=" CD GLU B 483 " pdb=" OE1 GLU B 483 " ideal model delta sinusoidal sigma weight residual 0.00 89.77 -89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1638 0.111 - 0.222: 22 0.222 - 0.334: 0 0.334 - 0.445: 1 0.445 - 0.556: 1 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C14 ERG B 901 " pdb=" C13 ERG B 901 " pdb=" C15 ERG B 901 " pdb=" C8 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.26 -2.82 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" C10 ERG B 901 " pdb=" C1 ERG B 901 " pdb=" C5 ERG B 901 " pdb=" C9 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.77 -2.38 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C13 ERG B 901 " pdb=" C12 ERG B 901 " pdb=" C14 ERG B 901 " pdb=" C17 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1659 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 901 " 0.146 2.00e-02 2.50e+03 1.47e-01 2.15e+02 pdb=" C22 ERG B 901 " -0.141 2.00e-02 2.50e+03 pdb=" C23 ERG B 901 " -0.152 2.00e-02 2.50e+03 pdb=" C24 ERG B 901 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 513 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 514 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 277 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.019 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1396 2.76 - 3.29: 10098 3.29 - 3.83: 18206 3.83 - 4.36: 21016 4.36 - 4.90: 37151 Nonbonded interactions: 87867 Sorted by model distance: nonbonded pdb=" O ALA B 573 " pdb=" OG SER B 591 " model vdw 2.221 3.040 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.271 3.040 nonbonded pdb=" OG SER B 428 " pdb=" OG1 THR B 515 " model vdw 2.292 3.040 nonbonded pdb=" OG SER B 428 " pdb=" O TYR B 511 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR B 293 " pdb=" O ALA B 296 " model vdw 2.312 3.040 ... (remaining 87862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.100 Find NCS groups from input model: 0.060 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10764 Z= 0.121 Angle : 0.563 7.876 14577 Z= 0.319 Chirality : 0.041 0.556 1662 Planarity : 0.005 0.147 1828 Dihedral : 14.721 89.774 3915 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.39 % Allowed : 16.67 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.22), residues: 1308 helix: 0.26 (0.19), residues: 681 sheet: -1.46 (0.33), residues: 178 loop : -2.63 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 108 TYR 0.008 0.001 TYR A 487 PHE 0.013 0.001 PHE B 493 TRP 0.005 0.001 TRP C 55 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.12 (10761) covalent geometry : angle 0.56112 / 0.32 (14571) SS BOND : bond 0.00147 / 0.10 ( 3) SS BOND : angle 2.07155 / 1.28 ( 6) hydrogen bonds : bond 0.12640 / 7.67 ( 591) hydrogen bonds : angle 5.27759 / 3.80 ( 1710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8706 (tmm) cc_final: 0.8408 (tmm) REVERT: B 146 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8391 (tttm) REVERT: B 156 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: B 517 TRP cc_start: 0.7264 (m100) cc_final: 0.6768 (t60) REVERT: B 577 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5841 (mtp) outliers start: 39 outliers final: 14 residues processed: 255 average time/residue: 0.4872 time to fit residues: 134.1838 Evaluate side-chains 167 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 GLN A 378 ASN A 425 GLN A 459 GLN A 462 GLN A 493 HIS A 578 ASN B 99 GLN B 155 ASN B 199 GLN B 249 HIS B 270 HIS B 271 GLN B 302 GLN B 409 ASN B 438 HIS B 568 ASN C 58 GLN C 75 ASN C 103 GLN D 26 GLN D 47 GLN D 58 GLN D 65 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.090862 restraints weight = 14502.846| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.09 r_work: 0.2955 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10764 Z= 0.117 Angle : 0.531 6.815 14577 Z= 0.268 Chirality : 0.039 0.147 1662 Planarity : 0.004 0.051 1828 Dihedral : 5.719 59.277 1489 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.25 % Allowed : 19.79 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1308 helix: 1.35 (0.20), residues: 689 sheet: -1.05 (0.35), residues: 182 loop : -1.84 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 44 TYR 0.015 0.001 TYR A 114 PHE 0.015 0.001 PHE A 585 TRP 0.008 0.001 TRP C 128 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (10761) covalent geometry : angle 0.53088 / 0.27 (14571) SS BOND : bond 0.00283 / 0.20 ( 3) SS BOND : angle 0.59554 / 0.31 ( 6) hydrogen bonds : bond 0.03779 / 2.48 ( 591) hydrogen bonds : angle 4.08367 / 2.92 ( 1710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.9032 (tmm) cc_final: 0.8739 (tmm) REVERT: A 529 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 630 PHE cc_start: 0.7274 (m-80) cc_final: 0.6988 (t80) REVERT: B 156 GLN cc_start: 0.7890 (pm20) cc_final: 0.7622 (pm20) REVERT: B 244 ASP cc_start: 0.7851 (t0) cc_final: 0.7625 (t70) REVERT: B 392 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7351 (mpp) REVERT: B 474 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 517 TRP cc_start: 0.7629 (m100) cc_final: 0.6720 (t60) REVERT: C 26 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8488 (m) REVERT: C 103 GLN cc_start: 0.8401 (tp40) cc_final: 0.7947 (tp40) outliers start: 49 outliers final: 21 residues processed: 193 average time/residue: 0.5242 time to fit residues: 109.1864 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 ASN A 410 ASN B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.081152 restraints weight = 14435.211| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.20 r_work: 0.2780 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10764 Z= 0.186 Angle : 0.610 8.874 14577 Z= 0.308 Chirality : 0.042 0.144 1662 Planarity : 0.004 0.053 1828 Dihedral : 5.170 54.745 1474 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.21 % Allowed : 18.84 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1308 helix: 1.59 (0.20), residues: 686 sheet: -0.74 (0.36), residues: 188 loop : -1.64 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 44 TYR 0.015 0.002 TYR A 114 PHE 0.018 0.002 PHE A 630 TRP 0.008 0.001 TRP B 598 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (10761) covalent geometry : angle 0.60958 / 0.31 (14571) SS BOND : bond 0.00370 / 0.26 ( 3) SS BOND : angle 1.00824 / 0.54 ( 6) hydrogen bonds : bond 0.05077 / 3.38 ( 591) hydrogen bonds : angle 4.19194 / 2.99 ( 1710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6963 (pm20) cc_final: 0.6698 (pm20) REVERT: B 121 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5608 (mmt-90) REVERT: B 244 ASP cc_start: 0.7942 (t0) cc_final: 0.7722 (t70) REVERT: B 392 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7561 (mpp) REVERT: B 427 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8309 (mmm) REVERT: B 441 ILE cc_start: 0.8864 (mt) cc_final: 0.8661 (mm) REVERT: B 474 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 517 TRP cc_start: 0.7819 (m100) cc_final: 0.7023 (t60) REVERT: B 582 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.7190 (p) REVERT: C 26 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8535 (m) REVERT: C 94 ASP cc_start: 0.8308 (t0) cc_final: 0.8013 (t0) REVERT: C 99 ILE cc_start: 0.8909 (mt) cc_final: 0.8461 (mp) REVERT: C 103 GLN cc_start: 0.8389 (tp40) cc_final: 0.7465 (tp-100) outliers start: 60 outliers final: 21 residues processed: 181 average time/residue: 0.4770 time to fit residues: 93.2779 Evaluate side-chains 154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 71 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.083017 restraints weight = 14525.168| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.09 r_work: 0.2819 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10764 Z= 0.135 Angle : 0.557 7.459 14577 Z= 0.282 Chirality : 0.040 0.144 1662 Planarity : 0.004 0.055 1828 Dihedral : 4.657 52.985 1469 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.43 % Allowed : 19.53 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1308 helix: 1.77 (0.20), residues: 687 sheet: -0.53 (0.37), residues: 188 loop : -1.44 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 44 TYR 0.016 0.001 TYR A 114 PHE 0.016 0.001 PHE B 493 TRP 0.007 0.001 TRP B 598 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10761) covalent geometry : angle 0.55716 / 0.28 (14571) SS BOND : bond 0.00313 / 0.21 ( 3) SS BOND : angle 0.72305 / 0.39 ( 6) hydrogen bonds : bond 0.04392 / 2.92 ( 591) hydrogen bonds : angle 4.05753 / 2.88 ( 1710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6951 (pm20) cc_final: 0.6692 (pm20) REVERT: A 334 ILE cc_start: 0.8079 (mm) cc_final: 0.7849 (mt) REVERT: A 345 MET cc_start: 0.7670 (pp-130) cc_final: 0.7090 (tpp) REVERT: A 647 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6422 (t70) REVERT: B 244 ASP cc_start: 0.7791 (t0) cc_final: 0.7556 (t70) REVERT: B 392 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7489 (mpp) REVERT: B 427 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8262 (mmm) REVERT: B 441 ILE cc_start: 0.8924 (mt) cc_final: 0.8712 (mm) REVERT: B 474 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 503 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: B 517 TRP cc_start: 0.7777 (m100) cc_final: 0.6956 (t60) REVERT: B 582 SER cc_start: 0.7555 (OUTLIER) cc_final: 0.7166 (p) REVERT: C 26 SER cc_start: 0.8892 (t) cc_final: 0.8525 (m) REVERT: C 32 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5840 (mm110) REVERT: C 94 ASP cc_start: 0.8333 (t0) cc_final: 0.8010 (t0) REVERT: C 99 ILE cc_start: 0.8879 (mt) cc_final: 0.8431 (mp) REVERT: C 103 GLN cc_start: 0.8316 (tp40) cc_final: 0.7488 (tp-100) REVERT: C 123 MET cc_start: 0.9118 (mmp) cc_final: 0.8904 (mmm) outliers start: 51 outliers final: 24 residues processed: 177 average time/residue: 0.4929 time to fit residues: 94.4806 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.078545 restraints weight = 14294.642| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.12 r_work: 0.2735 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10764 Z= 0.243 Angle : 0.644 9.489 14577 Z= 0.327 Chirality : 0.044 0.154 1662 Planarity : 0.004 0.056 1828 Dihedral : 5.018 53.491 1469 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.03 % Allowed : 18.92 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1308 helix: 1.63 (0.20), residues: 685 sheet: -0.46 (0.37), residues: 188 loop : -1.36 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 44 TYR 0.015 0.002 TYR A 570 PHE 0.019 0.002 PHE B 493 TRP 0.009 0.001 TRP B 584 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (10761) covalent geometry : angle 0.64404 / 0.33 (14571) SS BOND : bond 0.00402 / 0.28 ( 3) SS BOND : angle 1.04846 / 0.54 ( 6) hydrogen bonds : bond 0.05523 / 3.69 ( 591) hydrogen bonds : angle 4.25759 / 3.02 ( 1710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 135 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: A 345 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7148 (tpp) REVERT: A 647 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.6540 (t70) REVERT: B 26 ARG cc_start: 0.6340 (ptt180) cc_final: 0.6137 (ptt180) REVERT: B 244 ASP cc_start: 0.7977 (t0) cc_final: 0.7742 (t70) REVERT: B 392 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7514 (mpp) REVERT: B 441 ILE cc_start: 0.8880 (mt) cc_final: 0.8663 (mm) REVERT: B 474 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 503 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: B 517 TRP cc_start: 0.7799 (m100) cc_final: 0.6973 (t60) REVERT: B 582 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7291 (p) REVERT: C 26 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8518 (m) REVERT: C 88 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7542 (mtm-85) REVERT: C 94 ASP cc_start: 0.8392 (t0) cc_final: 0.8069 (t0) REVERT: C 99 ILE cc_start: 0.8872 (mt) cc_final: 0.8421 (mp) REVERT: C 103 GLN cc_start: 0.8348 (tp40) cc_final: 0.7586 (tp-100) REVERT: C 130 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: D 97 SER cc_start: 0.8283 (t) cc_final: 0.8003 (p) outliers start: 58 outliers final: 34 residues processed: 178 average time/residue: 0.5048 time to fit residues: 97.2137 Evaluate side-chains 172 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 5 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 HIS A 251 GLN B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.084436 restraints weight = 14370.396| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.07 r_work: 0.2847 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10764 Z= 0.110 Angle : 0.538 7.803 14577 Z= 0.273 Chirality : 0.039 0.141 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.622 53.740 1469 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.99 % Allowed : 20.31 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1308 helix: 1.97 (0.20), residues: 685 sheet: -0.34 (0.38), residues: 188 loop : -1.25 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 44 TYR 0.017 0.001 TYR A 114 PHE 0.015 0.001 PHE B 493 TRP 0.009 0.001 TRP A 461 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (10761) covalent geometry : angle 0.53802 / 0.27 (14571) SS BOND : bond 0.00272 / 0.17 ( 3) SS BOND : angle 0.60283 / 0.31 ( 6) hydrogen bonds : bond 0.03946 / 2.62 ( 591) hydrogen bonds : angle 3.98774 / 2.83 ( 1710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8061 (mm) cc_final: 0.7850 (mt) REVERT: A 345 MET cc_start: 0.7617 (pp-130) cc_final: 0.7083 (tpp) REVERT: A 353 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7387 (mmt) REVERT: A 529 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8829 (mp) REVERT: B 156 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: B 244 ASP cc_start: 0.7816 (t0) cc_final: 0.7581 (t70) REVERT: B 441 ILE cc_start: 0.8949 (mt) cc_final: 0.8732 (mm) REVERT: B 474 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 503 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: B 517 TRP cc_start: 0.7752 (m100) cc_final: 0.6949 (t60) REVERT: B 582 SER cc_start: 0.7424 (OUTLIER) cc_final: 0.7058 (p) REVERT: C 26 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8529 (m) REVERT: C 94 ASP cc_start: 0.8272 (t0) cc_final: 0.8042 (OUTLIER) REVERT: C 99 ILE cc_start: 0.8865 (mt) cc_final: 0.8423 (mp) REVERT: C 103 GLN cc_start: 0.8435 (tp40) cc_final: 0.7916 (tp40) REVERT: D 97 SER cc_start: 0.8209 (t) cc_final: 0.7980 (p) outliers start: 46 outliers final: 24 residues processed: 179 average time/residue: 0.5019 time to fit residues: 97.5439 Evaluate side-chains 164 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 40 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.082536 restraints weight = 14808.085| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.12 r_work: 0.2825 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10764 Z= 0.152 Angle : 0.580 7.653 14577 Z= 0.293 Chirality : 0.041 0.145 1662 Planarity : 0.004 0.057 1828 Dihedral : 4.680 48.244 1469 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.30 % Allowed : 21.35 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1308 helix: 1.95 (0.20), residues: 685 sheet: -0.28 (0.38), residues: 188 loop : -1.18 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 44 TYR 0.017 0.001 TYR A 114 PHE 0.017 0.001 PHE B 493 TRP 0.008 0.001 TRP B 598 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10761) covalent geometry : angle 0.57996 / 0.29 (14571) SS BOND : bond 0.00299 / 0.20 ( 3) SS BOND : angle 0.77226 / 0.41 ( 6) hydrogen bonds : bond 0.04580 / 3.05 ( 591) hydrogen bonds : angle 4.02845 / 2.86 ( 1710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6946 (pm20) cc_final: 0.6671 (pm20) REVERT: A 334 ILE cc_start: 0.8100 (mm) cc_final: 0.7886 (mt) REVERT: A 345 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7123 (tpp) REVERT: A 353 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7416 (mmt) REVERT: A 529 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8870 (mp) REVERT: A 647 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.6416 (t70) REVERT: B 156 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: B 244 ASP cc_start: 0.7906 (t0) cc_final: 0.7673 (t70) REVERT: B 392 MET cc_start: 0.7547 (mtt) cc_final: 0.7227 (mpp) REVERT: B 474 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 503 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: B 517 TRP cc_start: 0.7839 (m100) cc_final: 0.6988 (t60) REVERT: B 582 SER cc_start: 0.7516 (OUTLIER) cc_final: 0.7108 (p) REVERT: C 26 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8507 (m) REVERT: C 94 ASP cc_start: 0.8279 (t0) cc_final: 0.8001 (t0) REVERT: C 99 ILE cc_start: 0.8897 (mt) cc_final: 0.8461 (mp) REVERT: C 103 GLN cc_start: 0.8415 (tp40) cc_final: 0.7897 (tp40) REVERT: D 38 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7884 (ptm-80) REVERT: D 97 SER cc_start: 0.8238 (t) cc_final: 0.8006 (p) outliers start: 38 outliers final: 20 residues processed: 165 average time/residue: 0.5068 time to fit residues: 90.5916 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 27 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.079761 restraints weight = 14313.048| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.07 r_work: 0.2767 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10764 Z= 0.188 Angle : 0.611 8.111 14577 Z= 0.309 Chirality : 0.042 0.147 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.814 48.145 1469 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.56 % Allowed : 21.01 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1308 helix: 1.85 (0.20), residues: 683 sheet: -0.26 (0.38), residues: 188 loop : -1.19 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 44 TYR 0.016 0.002 TYR A 114 PHE 0.018 0.002 PHE B 493 TRP 0.008 0.001 TRP B 584 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (10761) covalent geometry : angle 0.61046 / 0.31 (14571) SS BOND : bond 0.00324 / 0.22 ( 3) SS BOND : angle 0.91676 / 0.47 ( 6) hydrogen bonds : bond 0.04972 / 3.32 ( 591) hydrogen bonds : angle 4.11819 / 2.92 ( 1710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6881 (pm20) cc_final: 0.6606 (pm20) REVERT: A 334 ILE cc_start: 0.8103 (mm) cc_final: 0.7884 (mt) REVERT: A 345 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7147 (tpp) REVERT: A 353 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7401 (mmm) REVERT: A 647 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6381 (t70) REVERT: B 156 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7417 (mm-40) REVERT: B 244 ASP cc_start: 0.7871 (t0) cc_final: 0.7642 (t70) REVERT: B 392 MET cc_start: 0.7598 (mtt) cc_final: 0.7279 (mpp) REVERT: B 441 ILE cc_start: 0.8984 (mt) cc_final: 0.8621 (mm) REVERT: B 474 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 503 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: B 517 TRP cc_start: 0.7790 (m100) cc_final: 0.6977 (t60) REVERT: B 582 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7214 (p) REVERT: C 26 SER cc_start: 0.8931 (t) cc_final: 0.8532 (m) REVERT: C 94 ASP cc_start: 0.8281 (t0) cc_final: 0.8009 (t0) REVERT: C 99 ILE cc_start: 0.8900 (mt) cc_final: 0.8442 (mp) REVERT: C 103 GLN cc_start: 0.8423 (tp40) cc_final: 0.7585 (tp-100) REVERT: D 97 SER cc_start: 0.8288 (t) cc_final: 0.8047 (p) outliers start: 41 outliers final: 23 residues processed: 166 average time/residue: 0.4576 time to fit residues: 82.4074 Evaluate side-chains 163 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.082253 restraints weight = 14229.979| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.14 r_work: 0.2804 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10764 Z= 0.132 Angle : 0.568 7.628 14577 Z= 0.287 Chirality : 0.040 0.142 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.643 46.581 1469 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.21 % Allowed : 21.18 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1308 helix: 2.01 (0.20), residues: 685 sheet: -0.21 (0.38), residues: 194 loop : -1.14 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 44 TYR 0.017 0.001 TYR A 114 PHE 0.017 0.001 PHE B 493 TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10761) covalent geometry : angle 0.56808 / 0.29 (14571) SS BOND : bond 0.00294 / 0.19 ( 3) SS BOND : angle 0.73870 / 0.39 ( 6) hydrogen bonds : bond 0.04314 / 2.87 ( 591) hydrogen bonds : angle 4.00560 / 2.84 ( 1710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6873 (pm20) cc_final: 0.6591 (pm20) REVERT: A 334 ILE cc_start: 0.8081 (mm) cc_final: 0.7860 (mt) REVERT: A 345 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7101 (tpp) REVERT: A 353 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7394 (mmm) REVERT: A 529 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8748 (mp) REVERT: B 156 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7421 (mm-40) REVERT: B 244 ASP cc_start: 0.7858 (t0) cc_final: 0.7632 (t70) REVERT: B 392 MET cc_start: 0.7505 (mtt) cc_final: 0.7207 (mpp) REVERT: B 474 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 503 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: B 517 TRP cc_start: 0.7741 (m100) cc_final: 0.6955 (t60) REVERT: B 582 SER cc_start: 0.7462 (OUTLIER) cc_final: 0.7063 (p) REVERT: C 26 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8515 (m) REVERT: C 94 ASP cc_start: 0.8231 (t0) cc_final: 0.7969 (t0) REVERT: C 99 ILE cc_start: 0.8862 (mt) cc_final: 0.8419 (mp) REVERT: C 103 GLN cc_start: 0.8391 (tp40) cc_final: 0.7524 (tp-100) REVERT: D 97 SER cc_start: 0.8280 (t) cc_final: 0.8042 (p) outliers start: 37 outliers final: 24 residues processed: 171 average time/residue: 0.4671 time to fit residues: 86.9268 Evaluate side-chains 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.083611 restraints weight = 14154.559| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.14 r_work: 0.2829 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10764 Z= 0.120 Angle : 0.560 8.603 14577 Z= 0.280 Chirality : 0.039 0.141 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.512 46.145 1469 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.95 % Allowed : 21.61 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1308 helix: 2.09 (0.20), residues: 690 sheet: -0.14 (0.38), residues: 194 loop : -1.07 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 44 TYR 0.016 0.001 TYR A 114 PHE 0.016 0.001 PHE B 493 TRP 0.009 0.001 TRP A 461 HIS 0.004 0.000 HIS B 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10761) covalent geometry : angle 0.56013 / 0.28 (14571) SS BOND : bond 0.00287 / 0.18 ( 3) SS BOND : angle 0.67352 / 0.36 ( 6) hydrogen bonds : bond 0.04067 / 2.70 ( 591) hydrogen bonds : angle 3.92421 / 2.78 ( 1710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6884 (pm20) cc_final: 0.6610 (pm20) REVERT: A 334 ILE cc_start: 0.8106 (mm) cc_final: 0.7883 (mt) REVERT: A 345 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7130 (tpp) REVERT: A 353 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7408 (mmm) REVERT: A 412 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7944 (tm) REVERT: A 529 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8793 (mp) REVERT: B 156 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7424 (mm-40) REVERT: B 474 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 503 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: B 517 TRP cc_start: 0.7760 (m100) cc_final: 0.6926 (t60) REVERT: B 582 SER cc_start: 0.7518 (OUTLIER) cc_final: 0.7115 (p) REVERT: C 26 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8512 (m) REVERT: C 94 ASP cc_start: 0.8263 (t0) cc_final: 0.7945 (t0) REVERT: C 99 ILE cc_start: 0.8877 (mt) cc_final: 0.8401 (mp) REVERT: C 103 GLN cc_start: 0.8389 (tp40) cc_final: 0.7554 (tp-100) REVERT: D 97 SER cc_start: 0.8267 (t) cc_final: 0.8039 (p) outliers start: 34 outliers final: 22 residues processed: 165 average time/residue: 0.5031 time to fit residues: 90.6116 Evaluate side-chains 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 129 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.082812 restraints weight = 14306.794| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.08 r_work: 0.2817 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10764 Z= 0.133 Angle : 0.578 8.557 14577 Z= 0.290 Chirality : 0.040 0.228 1662 Planarity : 0.004 0.058 1828 Dihedral : 4.539 45.907 1469 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.04 % Allowed : 21.79 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1308 helix: 2.10 (0.20), residues: 685 sheet: -0.14 (0.38), residues: 195 loop : -1.04 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 44 TYR 0.017 0.001 TYR A 114 PHE 0.031 0.001 PHE C 89 TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10761) covalent geometry : angle 0.57768 / 0.29 (14571) SS BOND : bond 0.00309 / 0.20 ( 3) SS BOND : angle 0.73921 / 0.40 ( 6) hydrogen bonds : bond 0.04268 / 2.84 ( 591) hydrogen bonds : angle 3.95126 / 2.80 ( 1710) =============================================================================== Job complete usr+sys time: 3773.93 seconds wall clock time: 64 minutes 58.28 seconds (3898.28 seconds total)