Starting phenix.real_space_refine on Thu Jul 2 06:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jzx_36754/07_2026/8jzx_36754.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.058 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 36 5.16 5 C 4760 2.51 5 N 1126 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7108 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3452 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3452 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'CLR': 2, 'NAG': 1, 'Q09': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'CLR': 2, 'NAG': 1, 'Q09': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.43, per 1000 atoms: 0.20 Number of scatterers: 7108 At special positions: 0 Unit cell: (80.9568, 59.031, 124.808, 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 36 16.00 O 1186 8.00 N 1126 7.00 C 4760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " 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=1, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 436 " " NAG B 601 " - " ASN B 436 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 415.3 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 2 sheets defined 81.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 33 through 56 removed outlier: 3.810A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 88 removed outlier: 3.568A pdb=" N TYR A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.836A pdb=" N ALA A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.661A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.513A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 181 removed outlier: 3.611A pdb=" N ALA A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.790A pdb=" N ALA A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 212 removed outlier: 3.649A pdb=" N ALA A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.631A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 244 Proline residue: A 229 - end of helix removed outlier: 3.857A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.561A pdb=" N VAL A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 328 through 348 removed outlier: 3.578A pdb=" N GLN A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.528A pdb=" N TRP A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 370 through 388 removed outlier: 4.607A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.601A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.568A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 3.511A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.728A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 510 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.689A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.810A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 88 removed outlier: 3.568A pdb=" N TYR B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 removed outlier: 3.836A pdb=" N ALA B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.661A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.513A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 181 removed outlier: 3.612A pdb=" N ALA B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 3.790A pdb=" N ALA B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 212 removed outlier: 3.648A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.631A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 Proline residue: B 229 - end of helix removed outlier: 3.857A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 removed outlier: 3.562A pdb=" N VAL B 319 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.577A pdb=" N GLN B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.528A pdb=" N TRP B 368 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 370 through 388 removed outlier: 4.607A pdb=" N ALA B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.600A pdb=" N HIS B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 430 removed outlier: 3.568A pdb=" N ARG B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 413 " --> pdb=" O MET B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 453 removed outlier: 3.511A pdb=" N TRP B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 450 through 453' Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.728A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 Processing helix chain 'B' and resid 531 through 558 removed outlier: 3.689A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 removed outlier: 3.834A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 435 through 439 removed outlier: 3.834A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1437 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: 1.10 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1048 1.31 - 1.43: 2025 1.43 - 1.56: 4165 1.56 - 1.68: 0 1.68 - 1.81: 54 Bond restraints: 7292 Sorted by residual: bond pdb=" C25 Q09 B 604 " pdb=" N26 Q09 B 604 " ideal model delta sigma weight residual 1.464 1.212 0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C25 Q09 A 603 " pdb=" N26 Q09 A 603 " ideal model delta sigma weight residual 1.464 1.212 0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C20 Q09 A 603 " pdb=" N22 Q09 A 603 " ideal model delta sigma weight residual 1.343 1.457 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C20 Q09 B 604 " pdb=" N22 Q09 B 604 " ideal model delta sigma weight residual 1.343 1.457 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C28 Q09 B 604 " pdb=" C29 Q09 B 604 " ideal model delta sigma weight residual 1.524 1.442 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 7287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 9507 2.33 - 4.65: 327 4.65 - 6.98: 79 6.98 - 9.31: 21 9.31 - 11.64: 6 Bond angle restraints: 9940 Sorted by residual: angle pdb=" C ALA B 29 " pdb=" N PHE B 30 " pdb=" CA PHE B 30 " ideal model delta sigma weight residual 121.54 133.18 -11.64 1.91e+00 2.74e-01 3.71e+01 angle pdb=" C ALA A 29 " pdb=" N PHE A 30 " pdb=" CA PHE A 30 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" C PHE A 30 " pdb=" N ALA A 31 " pdb=" CA ALA A 31 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C PHE B 30 " pdb=" N ALA B 31 " pdb=" CA ALA B 31 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C GLN B 485 " pdb=" N SER B 486 " pdb=" CA SER B 486 " ideal model delta sigma weight residual 121.54 130.07 -8.53 1.91e+00 2.74e-01 1.99e+01 ... (remaining 9935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 3986 16.73 - 33.45: 134 33.45 - 50.18: 28 50.18 - 66.91: 8 66.91 - 83.64: 6 Dihedral angle restraints: 4162 sinusoidal: 1566 harmonic: 2596 Sorted by residual: dihedral pdb=" CA PHE B 30 " pdb=" C PHE B 30 " pdb=" N ALA B 31 " pdb=" CA ALA B 31 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PHE A 30 " pdb=" C PHE A 30 " pdb=" N ALA A 31 " pdb=" CA ALA A 31 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO B 390 " pdb=" C PRO B 390 " pdb=" N ILE B 391 " pdb=" CA ILE B 391 " ideal model delta harmonic sigma weight residual 180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1058 0.082 - 0.164: 90 0.164 - 0.245: 18 0.245 - 0.327: 6 0.327 - 0.409: 4 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C13 CLR A 604 " pdb=" C12 CLR A 604 " pdb=" C14 CLR A 604 " pdb=" C17 CLR A 604 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C13 CLR B 602 " pdb=" C12 CLR B 602 " pdb=" C14 CLR B 602 " pdb=" C17 CLR B 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.53 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C14 CLR B 602 " pdb=" C13 CLR B 602 " pdb=" C15 CLR B 602 " pdb=" C8 CLR B 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1173 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 536 " -0.018 2.00e-02 2.50e+03 1.79e-02 5.58e+00 pdb=" CG PHE B 536 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 536 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 536 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 536 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 536 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 536 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 536 " 0.017 2.00e-02 2.50e+03 1.77e-02 5.49e+00 pdb=" CG PHE A 536 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 536 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 536 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 536 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 536 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 536 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 120 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 121 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.029 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2211 2.82 - 3.34: 6508 3.34 - 3.86: 11688 3.86 - 4.38: 14332 4.38 - 4.90: 24430 Nonbonded interactions: 59169 Sorted by model distance: nonbonded pdb=" C21 CLR A 602 " pdb=" C23 CLR A 602 " model vdw 2.300 3.088 nonbonded pdb=" C21 CLR B 603 " pdb=" C23 CLR B 603 " model vdw 2.301 3.088 nonbonded pdb=" O ALA A 27 " pdb=" NH1 ARG A 193 " model vdw 2.367 3.120 nonbonded pdb=" O ALA B 27 " pdb=" NH1 ARG B 193 " model vdw 2.368 3.120 nonbonded pdb=" O PHE B 30 " pdb=" N GLY B 32 " model vdw 2.385 3.120 ... (remaining 59164 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 602) selection = (chain 'B' and resid 18 through 602) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.140 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.011 0.491 7297 Z= 0.709 Angle : 1.136 11.637 9950 Z= 0.581 Chirality : 0.060 0.409 1176 Planarity : 0.007 0.050 1188 Dihedral : 10.492 83.636 2492 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.07 % Favored : 93.71 % Rotamer: Outliers : 0.28 % Allowed : 1.14 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.11 (0.16), residues: 890 helix: -4.21 (0.09), residues: 652 sheet: None (None), residues: 0 loop : -2.69 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 193 TYR 0.027 0.003 TYR B 113 PHE 0.040 0.003 PHE B 536 TRP 0.019 0.003 TRP B 368 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.42 ( 7292) covalent geometry : angle 1.13578 / 0.58 ( 9940) SS BOND : bond 0.00487 / 0.24 ( 2) SS BOND : angle 1.04926 / 0.57 ( 4) hydrogen bonds : bond 0.29394 / 19.33 ( 481) hydrogen bonds : angle 10.84573 / 7.31 ( 1437) Misc. bond : bond 0.49057 / 25.82 ( 1) link_NAG-ASN : bond 0.00138 / 0.07 ( 2) link_NAG-ASN : angle 1.87559 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.7655 (m-10) cc_final: 0.7366 (t80) REVERT: B 73 GLN cc_start: 0.7785 (mt0) cc_final: 0.7231 (mt0) REVERT: B 80 LEU cc_start: 0.8172 (mt) cc_final: 0.7948 (tm) REVERT: B 372 PHE cc_start: 0.7598 (m-10) cc_final: 0.7373 (m-10) REVERT: B 457 GLN cc_start: 0.8227 (mt0) cc_final: 0.7955 (mt0) outliers start: 2 outliers final: 1 residues processed: 169 average time/residue: 0.4708 time to fit residues: 84.5383 Evaluate side-chains 89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101284 restraints weight = 8475.718| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.94 r_work: 0.3156 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7297 Z= 0.152 Angle : 0.712 9.796 9950 Z= 0.361 Chirality : 0.041 0.195 1176 Planarity : 0.005 0.035 1188 Dihedral : 8.397 72.750 1048 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.72 % Favored : 94.83 % Rotamer: Outliers : 1.99 % Allowed : 9.69 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.24), residues: 890 helix: -1.25 (0.17), residues: 696 sheet: None (None), residues: 0 loop : -2.94 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 394 TYR 0.009 0.002 TYR A 86 PHE 0.018 0.002 PHE B 194 TRP 0.018 0.002 TRP A 453 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 7292) covalent geometry : angle 0.71164 / 0.36 ( 9940) SS BOND : bond 0.00351 / 0.18 ( 2) SS BOND : angle 0.82860 / 0.47 ( 4) hydrogen bonds : bond 0.05713 / 3.71 ( 481) hydrogen bonds : angle 4.98659 / 3.35 ( 1437) Misc. bond : bond 0.00184 / 0.10 ( 1) link_NAG-ASN : bond 0.00070 / 0.04 ( 2) link_NAG-ASN : angle 1.51611 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 453 TRP cc_start: 0.7655 (m100) cc_final: 0.7040 (m100) REVERT: A 465 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 84 LEU cc_start: 0.8477 (tp) cc_final: 0.8187 (tp) REVERT: B 151 ARG cc_start: 0.6922 (mtt90) cc_final: 0.6612 (mtp180) REVERT: B 379 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8914 (mm) REVERT: B 457 GLN cc_start: 0.8083 (mt0) cc_final: 0.7430 (mt0) REVERT: B 482 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8523 (tptt) outliers start: 14 outliers final: 1 residues processed: 105 average time/residue: 0.4262 time to fit residues: 47.5157 Evaluate side-chains 88 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 41 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099350 restraints weight = 8279.690| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.94 r_work: 0.3128 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7297 Z= 0.148 Angle : 0.650 10.012 9950 Z= 0.327 Chirality : 0.039 0.137 1176 Planarity : 0.004 0.035 1188 Dihedral : 7.232 58.352 1046 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.72 % Favored : 94.83 % Rotamer: Outliers : 1.14 % Allowed : 11.40 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.28), residues: 890 helix: 0.57 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 186 TYR 0.010 0.002 TYR A 52 PHE 0.015 0.002 PHE B 194 TRP 0.012 0.001 TRP B 197 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7292) covalent geometry : angle 0.64900 / 0.33 ( 9940) SS BOND : bond 0.00286 / 0.15 ( 2) SS BOND : angle 0.38726 / 0.23 ( 4) hydrogen bonds : bond 0.05283 / 3.43 ( 481) hydrogen bonds : angle 4.50833 / 3.04 ( 1437) Misc. bond : bond 0.00164 / 0.09 ( 1) link_NAG-ASN : bond 0.00039 / 0.02 ( 2) link_NAG-ASN : angle 1.52046 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.179 Fit side-chains REVERT: A 453 TRP cc_start: 0.8049 (m100) cc_final: 0.7265 (m100) REVERT: B 84 LEU cc_start: 0.8548 (tp) cc_final: 0.8281 (tp) REVERT: B 151 ARG cc_start: 0.7044 (mtt90) cc_final: 0.6673 (mtp180) REVERT: B 184 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8152 (ttpt) REVERT: B 457 GLN cc_start: 0.8057 (mt0) cc_final: 0.7272 (mt0) REVERT: B 482 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8614 (tptt) REVERT: B 513 LYS cc_start: 0.7388 (ptpp) cc_final: 0.7128 (ttpt) outliers start: 8 outliers final: 2 residues processed: 99 average time/residue: 0.3854 time to fit residues: 40.5919 Evaluate side-chains 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098873 restraints weight = 8395.047| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.93 r_work: 0.3119 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7297 Z= 0.144 Angle : 0.641 9.754 9950 Z= 0.318 Chirality : 0.040 0.157 1176 Planarity : 0.004 0.035 1188 Dihedral : 6.548 50.640 1046 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.27 % Favored : 95.28 % Rotamer: Outliers : 1.57 % Allowed : 11.97 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.29), residues: 890 helix: 1.32 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.37 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 404 TYR 0.009 0.001 TYR A 52 PHE 0.017 0.002 PHE A 30 TRP 0.012 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7292) covalent geometry : angle 0.64050 / 0.32 ( 9940) SS BOND : bond 0.00071 / 0.04 ( 2) SS BOND : angle 0.31538 / 0.18 ( 4) hydrogen bonds : bond 0.04930 / 3.20 ( 481) hydrogen bonds : angle 4.36434 / 2.95 ( 1437) Misc. bond : bond 0.00216 / 0.11 ( 1) link_NAG-ASN : bond 0.00053 / 0.03 ( 2) link_NAG-ASN : angle 1.50597 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 GLN cc_start: 0.8232 (mt0) cc_final: 0.7900 (mt0) REVERT: B 84 LEU cc_start: 0.8528 (tp) cc_final: 0.8264 (tp) REVERT: B 151 ARG cc_start: 0.7173 (mtt90) cc_final: 0.6625 (mtt90) REVERT: B 184 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8075 (ttpt) REVERT: B 457 GLN cc_start: 0.7952 (mt0) cc_final: 0.7143 (mt0) outliers start: 11 outliers final: 6 residues processed: 97 average time/residue: 0.3904 time to fit residues: 40.4805 Evaluate side-chains 87 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097394 restraints weight = 8424.843| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.93 r_work: 0.3101 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7297 Z= 0.148 Angle : 0.642 10.126 9950 Z= 0.317 Chirality : 0.040 0.142 1176 Planarity : 0.004 0.058 1188 Dihedral : 6.381 51.702 1046 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.72 % Favored : 94.83 % Rotamer: Outliers : 2.14 % Allowed : 11.68 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 890 helix: 1.56 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.25 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 404 TYR 0.010 0.001 TYR A 52 PHE 0.016 0.002 PHE A 30 TRP 0.011 0.001 TRP B 197 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7292) covalent geometry : angle 0.64101 / 0.32 ( 9940) SS BOND : bond 0.00100 / 0.05 ( 2) SS BOND : angle 0.25011 / 0.14 ( 4) hydrogen bonds : bond 0.04950 / 3.21 ( 481) hydrogen bonds : angle 4.30905 / 2.93 ( 1437) Misc. bond : bond 0.00206 / 0.11 ( 1) link_NAG-ASN : bond 0.00081 / 0.04 ( 2) link_NAG-ASN : angle 1.54344 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 GLN cc_start: 0.8272 (mt0) cc_final: 0.7930 (mt0) REVERT: B 84 LEU cc_start: 0.8490 (tp) cc_final: 0.8231 (tp) REVERT: B 151 ARG cc_start: 0.7249 (mtt90) cc_final: 0.6768 (mtt90) REVERT: B 457 GLN cc_start: 0.7919 (mt0) cc_final: 0.7342 (mt0) outliers start: 15 outliers final: 7 residues processed: 96 average time/residue: 0.3729 time to fit residues: 38.5330 Evaluate side-chains 87 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099706 restraints weight = 8401.958| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.92 r_work: 0.3137 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7297 Z= 0.124 Angle : 0.612 9.419 9950 Z= 0.303 Chirality : 0.039 0.149 1176 Planarity : 0.004 0.057 1188 Dihedral : 6.136 51.017 1046 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.83 % Favored : 94.72 % Rotamer: Outliers : 1.57 % Allowed : 12.54 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 890 helix: 1.76 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.21 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.010 0.001 TYR A 52 PHE 0.017 0.001 PHE B 120 TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7292) covalent geometry : angle 0.61078 / 0.30 ( 9940) SS BOND : bond 0.00058 / 0.03 ( 2) SS BOND : angle 0.30116 / 0.17 ( 4) hydrogen bonds : bond 0.04443 / 2.89 ( 481) hydrogen bonds : angle 4.20499 / 2.85 ( 1437) Misc. bond : bond 0.00143 / 0.08 ( 1) link_NAG-ASN : bond 0.00071 / 0.04 ( 2) link_NAG-ASN : angle 1.55209 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 GLN cc_start: 0.8123 (mt0) cc_final: 0.7832 (mt0) REVERT: B 151 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6684 (mtt90) outliers start: 11 outliers final: 5 residues processed: 91 average time/residue: 0.3685 time to fit residues: 36.0035 Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 0.0670 chunk 78 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102078 restraints weight = 8395.759| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.91 r_work: 0.3171 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7297 Z= 0.117 Angle : 0.598 10.002 9950 Z= 0.294 Chirality : 0.038 0.131 1176 Planarity : 0.004 0.052 1188 Dihedral : 5.894 50.116 1046 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.16 % Favored : 95.39 % Rotamer: Outliers : 1.42 % Allowed : 13.11 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.29), residues: 890 helix: 1.95 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -2.24 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 193 TYR 0.010 0.001 TYR B 335 PHE 0.014 0.001 PHE A 30 TRP 0.009 0.001 TRP A 197 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 7292) covalent geometry : angle 0.59749 / 0.29 ( 9940) SS BOND : bond 0.00032 / 0.02 ( 2) SS BOND : angle 0.30408 / 0.17 ( 4) hydrogen bonds : bond 0.04115 / 2.68 ( 481) hydrogen bonds : angle 4.11297 / 2.79 ( 1437) Misc. bond : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : bond 0.00041 / 0.02 ( 2) link_NAG-ASN : angle 1.56467 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8090 (m-80) cc_final: 0.7586 (m-80) REVERT: A 457 GLN cc_start: 0.8082 (mt0) cc_final: 0.7822 (mt0) REVERT: A 501 PHE cc_start: 0.7584 (m-10) cc_final: 0.7371 (m-10) REVERT: B 84 LEU cc_start: 0.8510 (tp) cc_final: 0.8226 (tp) REVERT: B 151 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6664 (mtt90) REVERT: B 457 GLN cc_start: 0.7800 (mt0) cc_final: 0.7219 (mt0) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.3887 time to fit residues: 38.2556 Evaluate side-chains 80 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100659 restraints weight = 8418.639| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.93 r_work: 0.3153 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7297 Z= 0.125 Angle : 0.616 9.350 9950 Z= 0.301 Chirality : 0.038 0.133 1176 Planarity : 0.004 0.049 1188 Dihedral : 5.916 50.175 1046 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.51 % Rotamer: Outliers : 1.42 % Allowed : 13.82 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.29), residues: 890 helix: 2.00 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -2.08 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.011 0.001 TYR B 335 PHE 0.014 0.001 PHE B 120 TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7292) covalent geometry : angle 0.61497 / 0.30 ( 9940) SS BOND : bond 0.00051 / 0.03 ( 2) SS BOND : angle 0.28101 / 0.15 ( 4) hydrogen bonds : bond 0.04339 / 2.83 ( 481) hydrogen bonds : angle 4.13997 / 2.81 ( 1437) Misc. bond : bond 0.00114 / 0.06 ( 1) link_NAG-ASN : bond 0.00068 / 0.03 ( 2) link_NAG-ASN : angle 1.51109 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8076 (m-80) cc_final: 0.7585 (m-80) REVERT: A 457 GLN cc_start: 0.8133 (mt0) cc_final: 0.7871 (mt0) REVERT: A 501 PHE cc_start: 0.7519 (m-10) cc_final: 0.7306 (m-10) REVERT: B 151 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6648 (mtt90) REVERT: B 453 TRP cc_start: 0.7884 (m100) cc_final: 0.7666 (m100) REVERT: B 457 GLN cc_start: 0.7861 (mt0) cc_final: 0.7377 (mt0) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.4103 time to fit residues: 36.5030 Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097880 restraints weight = 8336.771| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.92 r_work: 0.3111 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7297 Z= 0.148 Angle : 0.646 9.031 9950 Z= 0.316 Chirality : 0.040 0.147 1176 Planarity : 0.004 0.045 1188 Dihedral : 6.103 56.029 1046 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.38 % Favored : 95.17 % Rotamer: Outliers : 1.57 % Allowed : 14.25 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.29), residues: 890 helix: 1.95 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.91 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.010 0.001 TYR A 52 PHE 0.018 0.001 PHE B 120 TRP 0.010 0.001 TRP B 197 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7292) covalent geometry : angle 0.64571 / 0.32 ( 9940) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.29495 / 0.16 ( 4) hydrogen bonds : bond 0.04816 / 3.13 ( 481) hydrogen bonds : angle 4.20538 / 2.86 ( 1437) Misc. bond : bond 0.00106 / 0.06 ( 1) link_NAG-ASN : bond 0.00114 / 0.06 ( 2) link_NAG-ASN : angle 1.48443 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 457 GLN cc_start: 0.8212 (mt0) cc_final: 0.7877 (mt0) REVERT: A 501 PHE cc_start: 0.7525 (m-10) cc_final: 0.7301 (m-10) REVERT: B 151 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6551 (mtt90) REVERT: B 457 GLN cc_start: 0.7926 (mt0) cc_final: 0.7275 (mt0) outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 0.4223 time to fit residues: 38.4538 Evaluate side-chains 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.0020 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 71 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099953 restraints weight = 8341.710| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.93 r_work: 0.3145 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7297 Z= 0.127 Angle : 0.631 9.371 9950 Z= 0.307 Chirality : 0.039 0.145 1176 Planarity : 0.004 0.042 1188 Dihedral : 6.040 56.521 1046 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.51 % Rotamer: Outliers : 1.14 % Allowed : 14.39 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.29), residues: 890 helix: 1.99 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.95 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.012 0.001 TYR B 335 PHE 0.021 0.001 PHE B 120 TRP 0.020 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7292) covalent geometry : angle 0.63033 / 0.31 ( 9940) SS BOND : bond 0.00040 / 0.02 ( 2) SS BOND : angle 0.32721 / 0.18 ( 4) hydrogen bonds : bond 0.04378 / 2.85 ( 481) hydrogen bonds : angle 4.15675 / 2.82 ( 1437) Misc. bond : bond 0.00347 / 0.18 ( 1) link_NAG-ASN : bond 0.00084 / 0.04 ( 2) link_NAG-ASN : angle 1.53165 / 0.79 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8115 (m-80) cc_final: 0.7685 (m-80) REVERT: A 457 GLN cc_start: 0.8127 (mt0) cc_final: 0.7823 (mt0) REVERT: A 501 PHE cc_start: 0.7521 (m-10) cc_final: 0.7291 (m-10) REVERT: B 151 ARG cc_start: 0.7133 (mtt90) cc_final: 0.6560 (mtt90) REVERT: B 457 GLN cc_start: 0.7860 (mt0) cc_final: 0.7234 (mt0) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.3976 time to fit residues: 35.4834 Evaluate side-chains 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097944 restraints weight = 8369.323| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.92 r_work: 0.3114 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7297 Z= 0.145 Angle : 0.654 8.980 9950 Z= 0.318 Chirality : 0.040 0.146 1176 Planarity : 0.004 0.038 1188 Dihedral : 6.152 57.844 1046 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.38 % Favored : 95.17 % Rotamer: Outliers : 1.42 % Allowed : 13.82 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.29), residues: 890 helix: 1.95 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.90 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.011 0.001 TYR B 335 PHE 0.022 0.001 PHE B 120 TRP 0.020 0.001 TRP B 453 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7292) covalent geometry : angle 0.65309 / 0.32 ( 9940) SS BOND : bond 0.00080 / 0.04 ( 2) SS BOND : angle 0.31284 / 0.17 ( 4) hydrogen bonds : bond 0.04757 / 3.10 ( 481) hydrogen bonds : angle 4.20519 / 2.86 ( 1437) Misc. bond : bond 0.00410 / 0.22 ( 1) link_NAG-ASN : bond 0.00118 / 0.06 ( 2) link_NAG-ASN : angle 1.50972 / 0.77 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.03 seconds wall clock time: 38 minutes 3.96 seconds (2283.96 seconds total)