Starting phenix.real_space_refine on Fri Jul 3 20:32:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ow8_13095/07_2026/7ow8_13095.cif" } resolution = 3.5 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= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8748 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5714 2.51 5 N 1490 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 8942 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4439 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain: "B" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4439 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 8942 At special positions: 0 Unit cell: (74.692, 85.212, 135.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1694 8.00 N 1490 7.00 C 5714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 236.8 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 71.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.651A pdb=" N PHE A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 50 removed outlier: 4.236A pdb=" N PHE A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 52 through 64 removed outlier: 4.158A pdb=" N SER A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 108 removed outlier: 3.713A pdb=" N LEU A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 4.046A pdb=" N PHE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.876A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 4.559A pdb=" N GLU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 163 removed outlier: 3.695A pdb=" N GLY A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 210 Proline residue: A 175 - end of helix Proline residue: A 183 - end of helix removed outlier: 4.159A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.840A pdb=" N GLU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 277 removed outlier: 3.883A pdb=" N LEU A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 3.519A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 315 removed outlier: 3.560A pdb=" N MET A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.690A pdb=" N ALA A 322 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 323 " --> pdb=" O ILE A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 444 through 455 removed outlier: 3.520A pdb=" N LYS A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.775A pdb=" N LYS A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.782A pdb=" N GLY A 476 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 495 removed outlier: 4.131A pdb=" N ARG A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.780A pdb=" N THR A 539 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 540 " --> pdb=" O LEU A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 540' Processing helix chain 'A' and resid 559 through 567 Processing helix chain 'A' and resid 570 through 586 removed outlier: 3.598A pdb=" N ALA A 574 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.652A pdb=" N PHE B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 50 removed outlier: 4.236A pdb=" N PHE B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 52 through 64 removed outlier: 4.158A pdb=" N SER B 58 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 108 removed outlier: 3.713A pdb=" N LEU B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 4.046A pdb=" N PHE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.699A pdb=" N THR B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.935A pdb=" N ILE B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 163 removed outlier: 3.749A pdb=" N MET B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 206 Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix removed outlier: 4.159A pdb=" N GLU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 200 " --> pdb=" O GLN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 221 through 248 removed outlier: 3.959A pdb=" N GLU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 277 removed outlier: 3.883A pdb=" N LEU B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 removed outlier: 3.519A pdb=" N LEU B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 315 removed outlier: 3.560A pdb=" N MET B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.690A pdb=" N ALA B 322 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 323 " --> pdb=" O ILE B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 323' Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 409 through 415 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.775A pdb=" N LYS B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.783A pdb=" N GLY B 476 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 495 removed outlier: 4.132A pdb=" N ARG B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 536 through 540 removed outlier: 3.780A pdb=" N THR B 539 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 536 through 540' Processing helix chain 'B' and resid 559 through 567 Processing helix chain 'B' and resid 570 through 586 removed outlier: 3.597A pdb=" N ALA B 574 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU B 584 " --> pdb=" O MET B 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348 removed outlier: 4.997A pdb=" N VAL A 346 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 420 removed outlier: 6.295A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 546 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG A 557 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 548 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 348 removed outlier: 4.997A pdb=" N VAL B 346 " --> pdb=" O GLU B 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 420 removed outlier: 6.295A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 546 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 557 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 548 " --> pdb=" O THR B 555 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1632 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: 1.35 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1471 1.28 - 1.42: 2086 1.42 - 1.55: 5426 1.55 - 1.68: 25 1.68 - 1.81: 70 Bond restraints: 9078 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.04e+01 bond pdb=" C ARG B 201 " pdb=" O ARG B 201 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.25e-02 6.40e+03 4.62e+01 bond pdb=" C THR A 131 " pdb=" O THR A 131 " ideal model delta sigma weight residual 1.237 1.310 -0.073 1.17e-02 7.31e+03 3.91e+01 bond pdb=" CA SER A 421 " pdb=" CB SER A 421 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.48e-02 4.57e+03 3.75e+01 ... (remaining 9073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 11996 4.54 - 9.09: 262 9.09 - 13.63: 37 13.63 - 18.17: 3 18.17 - 22.72: 4 Bond angle restraints: 12302 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.15 22.72 1.00e+00 1.00e+00 5.16e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 117.17 22.70 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.62 19.21 1.00e+00 1.00e+00 3.69e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 117.63 19.20 1.00e+00 1.00e+00 3.69e+02 angle pdb=" N THR A 203 " pdb=" CA THR A 203 " pdb=" C THR A 203 " ideal model delta sigma weight residual 112.90 97.66 15.24 1.31e+00 5.83e-01 1.35e+02 ... (remaining 12297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4675 16.92 - 33.83: 595 33.83 - 50.75: 139 50.75 - 67.66: 37 67.66 - 84.58: 16 Dihedral angle restraints: 5462 sinusoidal: 2156 harmonic: 3306 Sorted by residual: dihedral pdb=" C LYS A 238 " pdb=" N LYS A 238 " pdb=" CA LYS A 238 " pdb=" CB LYS A 238 " ideal model delta harmonic sigma weight residual -122.60 -150.91 28.31 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" N LYS A 238 " pdb=" C LYS A 238 " pdb=" CA LYS A 238 " pdb=" CB LYS A 238 " ideal model delta harmonic sigma weight residual 122.80 146.89 -24.09 0 2.50e+00 1.60e-01 9.28e+01 dihedral pdb=" C PHE B 202 " pdb=" N PHE B 202 " pdb=" CA PHE B 202 " pdb=" CB PHE B 202 " ideal model delta harmonic sigma weight residual -122.60 -145.76 23.16 0 2.50e+00 1.60e-01 8.58e+01 ... (remaining 5459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 1435 0.218 - 0.435: 38 0.435 - 0.653: 9 0.653 - 0.870: 0 0.870 - 1.088: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CA LYS A 238 " pdb=" N LYS A 238 " pdb=" C LYS A 238 " pdb=" CB LYS A 238 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA PHE B 202 " pdb=" N PHE B 202 " pdb=" C PHE B 202 " pdb=" CB PHE B 202 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA LYS B 230 " pdb=" N LYS B 230 " pdb=" C LYS B 230 " pdb=" CB LYS B 230 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 1481 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 118 " 0.028 2.00e-02 2.50e+03 5.80e-02 3.37e+01 pdb=" C ASN B 118 " -0.100 2.00e-02 2.50e+03 pdb=" O ASN B 118 " 0.038 2.00e-02 2.50e+03 pdb=" N ALA B 119 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 202 " -0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C PHE A 202 " 0.095 2.00e-02 2.50e+03 pdb=" O PHE A 202 " -0.034 2.00e-02 2.50e+03 pdb=" N THR A 203 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 227 " 0.027 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C GLY A 227 " -0.087 2.00e-02 2.50e+03 pdb=" O GLY A 227 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 228 " 0.029 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 97 2.57 - 3.15: 7301 3.15 - 3.73: 14031 3.73 - 4.32: 18876 4.32 - 4.90: 30161 Nonbonded interactions: 70466 Sorted by model distance: nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 1.983 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.984 2.170 nonbonded pdb=" OE1 GLN A 422 " pdb="MG MG A 602 " model vdw 2.038 2.170 nonbonded pdb=" OE1 GLN B 422 " pdb="MG MG B 602 " model vdw 2.038 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 2.046 2.170 ... (remaining 70461 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.950 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 0.091 9078 Z= 0.641 Angle : 1.608 22.715 12302 Z= 1.079 Chirality : 0.097 1.088 1484 Planarity : 0.010 0.078 1536 Dihedral : 16.656 84.579 3338 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 4.22 % Allowed : 8.13 % Favored : 87.65 % Cbeta Deviations : 2.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -3.90 (0.19), residues: 1150 helix: -2.36 (0.14), residues: 750 sheet: -1.83 (0.55), residues: 66 loop : -2.81 (0.27), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 484 TYR 0.032 0.003 TYR B 419 PHE 0.032 0.003 PHE A 384 TRP 0.007 0.002 TRP B 104 HIS 0.004 0.002 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.01109 / 0.64 ( 9078) covalent geometry : angle 1.60777 / 1.08 (12302) hydrogen bonds : bond 0.17789 / 11.42 ( 559) hydrogen bonds : angle 8.17112 / 5.80 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8761 (tp) cc_final: 0.8560 (tp) REVERT: A 105 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8026 (tttm) REVERT: A 129 ASN cc_start: 0.7975 (m-40) cc_final: 0.7693 (m110) REVERT: A 207 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7815 (t0) REVERT: A 231 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7338 (mtp) REVERT: A 238 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7147 (mtpt) REVERT: A 315 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 316 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7149 (mmm160) REVERT: A 334 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 365 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 408 TYR cc_start: 0.8690 (m-80) cc_final: 0.8117 (m-80) REVERT: A 447 GLU cc_start: 0.7661 (tp30) cc_final: 0.7453 (tp30) REVERT: A 453 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7729 (tp30) REVERT: A 506 THR cc_start: 0.7604 (p) cc_final: 0.7337 (t) REVERT: A 514 GLU cc_start: 0.7897 (tt0) cc_final: 0.7607 (tt0) REVERT: A 551 LYS cc_start: 0.8871 (mttt) cc_final: 0.8274 (mptt) REVERT: B 33 LEU cc_start: 0.8783 (mp) cc_final: 0.8557 (mp) REVERT: B 80 LEU cc_start: 0.8802 (tp) cc_final: 0.8581 (tp) REVERT: B 105 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8003 (tptp) REVERT: B 129 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: B 136 GLU cc_start: 0.8022 (pt0) cc_final: 0.7612 (tp30) REVERT: B 207 ASN cc_start: 0.8452 (t0) cc_final: 0.8052 (t0) REVERT: B 231 MET cc_start: 0.7615 (ttm) cc_final: 0.7311 (mtp) REVERT: B 234 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7077 (m) REVERT: B 315 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 316 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7145 (mmm160) REVERT: B 365 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 447 GLU cc_start: 0.7606 (tp30) cc_final: 0.7142 (tp30) REVERT: B 453 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7942 (tp30) REVERT: B 514 GLU cc_start: 0.7857 (tt0) cc_final: 0.7633 (tt0) REVERT: B 551 LYS cc_start: 0.8893 (mttt) cc_final: 0.8304 (mptt) REVERT: B 572 ASP cc_start: 0.7970 (m-30) cc_final: 0.7640 (m-30) outliers start: 41 outliers final: 12 residues processed: 225 average time/residue: 0.0944 time to fit residues: 28.2815 Evaluate side-chains 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS A 220 ASN A 247 GLN B 91 ASN B 129 ASN B 220 ASN B 519 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.200388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152398 restraints weight = 10297.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151165 restraints weight = 7763.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153501 restraints weight = 7302.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154000 restraints weight = 5031.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154781 restraints weight = 4751.620| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9078 Z= 0.201 Angle : 0.698 7.026 12302 Z= 0.373 Chirality : 0.044 0.180 1484 Planarity : 0.005 0.070 1536 Dihedral : 8.217 59.692 1271 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 4.22 % Allowed : 12.45 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -1.96 (0.23), residues: 1150 helix: -0.66 (0.18), residues: 748 sheet: -1.41 (0.59), residues: 66 loop : -2.50 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 345 TYR 0.014 0.002 TYR B 419 PHE 0.018 0.002 PHE A 573 TRP 0.009 0.001 TRP B 164 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 9078) covalent geometry : angle 0.69778 / 0.37 (12302) hydrogen bonds : bond 0.04780 / 3.22 ( 559) hydrogen bonds : angle 5.57737 / 3.94 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8772 (tp) cc_final: 0.8391 (tt) REVERT: A 127 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7652 (m) REVERT: A 238 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7347 (mtpt) REVERT: A 315 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 427 MET cc_start: 0.8478 (mtp) cc_final: 0.8191 (mtt) REVERT: A 453 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 454 MET cc_start: 0.7964 (mtt) cc_final: 0.7548 (ttm) REVERT: A 551 LYS cc_start: 0.8758 (mttt) cc_final: 0.8275 (mptt) REVERT: B 80 LEU cc_start: 0.8855 (tp) cc_final: 0.8607 (tp) REVERT: B 241 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7227 (m) REVERT: B 453 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7764 (tp30) REVERT: B 551 LYS cc_start: 0.8840 (mttt) cc_final: 0.8384 (mptt) outliers start: 41 outliers final: 16 residues processed: 183 average time/residue: 0.0784 time to fit residues: 20.0312 Evaluate side-chains 152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 423 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.0050 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A 338 HIS ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 519 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.204495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156156 restraints weight = 10331.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155291 restraints weight = 7798.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157928 restraints weight = 7239.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157862 restraints weight = 5025.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158435 restraints weight = 5283.152| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9078 Z= 0.134 Angle : 0.611 7.629 12302 Z= 0.324 Chirality : 0.041 0.161 1484 Planarity : 0.005 0.069 1536 Dihedral : 7.131 58.760 1251 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 2.88 % Allowed : 16.98 % Favored : 80.14 % 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: -0.93 (0.24), residues: 1150 helix: 0.09 (0.19), residues: 760 sheet: -0.92 (0.65), residues: 64 loop : -2.07 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.013 0.001 TYR A 83 PHE 0.018 0.001 PHE A 31 TRP 0.008 0.001 TRP B 164 HIS 0.021 0.002 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9078) covalent geometry : angle 0.61095 / 0.32 (12302) hydrogen bonds : bond 0.04041 / 2.71 ( 559) hydrogen bonds : angle 4.97087 / 3.51 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8822 (tp) cc_final: 0.8610 (tp) REVERT: A 127 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7296 (t) REVERT: A 238 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7451 (mtpt) REVERT: A 299 GLN cc_start: 0.7584 (mm110) cc_final: 0.7354 (mm-40) REVERT: A 315 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 453 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 454 MET cc_start: 0.7843 (mtt) cc_final: 0.7532 (ttm) REVERT: A 551 LYS cc_start: 0.8791 (mttt) cc_final: 0.8348 (mptt) REVERT: B 80 LEU cc_start: 0.8820 (tp) cc_final: 0.8567 (tp) REVERT: B 241 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7156 (m) REVERT: B 368 LYS cc_start: 0.8637 (mttp) cc_final: 0.8350 (mttm) REVERT: B 453 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7581 (tm-30) REVERT: B 454 MET cc_start: 0.8204 (ttm) cc_final: 0.7689 (ttt) REVERT: B 551 LYS cc_start: 0.8822 (mttt) cc_final: 0.8431 (mptt) outliers start: 28 outliers final: 17 residues processed: 172 average time/residue: 0.0808 time to fit residues: 19.3816 Evaluate side-chains 155 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 423 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 338 HIS B 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.197106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148933 restraints weight = 10504.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148790 restraints weight = 7941.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150346 restraints weight = 8208.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151679 restraints weight = 5601.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152064 restraints weight = 5150.416| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9078 Z= 0.232 Angle : 0.670 7.229 12302 Z= 0.354 Chirality : 0.045 0.162 1484 Planarity : 0.005 0.071 1536 Dihedral : 7.026 59.850 1251 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 3.81 % Allowed : 17.70 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.25), residues: 1150 helix: 0.38 (0.19), residues: 744 sheet: -0.94 (0.67), residues: 66 loop : -1.66 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.015 0.002 TYR A 83 PHE 0.027 0.002 PHE B 31 TRP 0.004 0.001 TRP A 413 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 ( 9078) covalent geometry : angle 0.67028 / 0.35 (12302) hydrogen bonds : bond 0.04270 / 2.88 ( 559) hydrogen bonds : angle 4.99730 / 3.53 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.260 Fit side-chains REVERT: A 127 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7443 (t) REVERT: A 238 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7470 (mtpt) REVERT: A 243 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 315 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 453 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7601 (tp30) REVERT: A 551 LYS cc_start: 0.8818 (mttt) cc_final: 0.8396 (mptt) REVERT: B 80 LEU cc_start: 0.8855 (tp) cc_final: 0.8605 (tp) REVERT: B 127 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7779 (m) REVERT: B 241 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.7132 (m) REVERT: B 243 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 299 GLN cc_start: 0.7528 (mm110) cc_final: 0.7300 (mm-40) REVERT: B 368 LYS cc_start: 0.8613 (mttp) cc_final: 0.8385 (mttm) REVERT: B 453 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 487 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.6672 (tt) REVERT: B 551 LYS cc_start: 0.8873 (mttt) cc_final: 0.8483 (mptt) outliers start: 37 outliers final: 21 residues processed: 180 average time/residue: 0.0806 time to fit residues: 20.2122 Evaluate side-chains 160 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 338 HIS B 91 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.201709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152571 restraints weight = 10266.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.151979 restraints weight = 7805.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154488 restraints weight = 6570.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.154980 restraints weight = 4664.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155194 restraints weight = 4622.281| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9078 Z= 0.149 Angle : 0.601 7.087 12302 Z= 0.316 Chirality : 0.042 0.177 1484 Planarity : 0.004 0.070 1536 Dihedral : 6.733 59.202 1251 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 3.70 % Allowed : 20.37 % Favored : 75.93 % 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: -0.10 (0.25), residues: 1150 helix: 0.75 (0.20), residues: 740 sheet: -0.84 (0.67), residues: 66 loop : -1.61 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 345 TYR 0.012 0.001 TYR B 83 PHE 0.027 0.001 PHE A 31 TRP 0.005 0.001 TRP A 164 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 9078) covalent geometry : angle 0.60109 / 0.32 (12302) hydrogen bonds : bond 0.03816 / 2.56 ( 559) hydrogen bonds : angle 4.68617 / 3.30 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.234 Fit side-chains REVERT: A 127 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7546 (p) REVERT: A 238 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7213 (mtpt) REVERT: A 243 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 315 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 368 LYS cc_start: 0.8404 (mttm) cc_final: 0.8192 (mttm) REVERT: A 453 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 454 MET cc_start: 0.8167 (ttm) cc_final: 0.7671 (ttm) REVERT: A 551 LYS cc_start: 0.8827 (mttt) cc_final: 0.8352 (mptt) REVERT: B 80 LEU cc_start: 0.8806 (tp) cc_final: 0.8546 (tp) REVERT: B 127 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7806 (m) REVERT: B 243 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 299 GLN cc_start: 0.7440 (mm110) cc_final: 0.7227 (mm-40) REVERT: B 365 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 368 LYS cc_start: 0.8641 (mttp) cc_final: 0.8398 (mttm) REVERT: B 453 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7653 (tm-30) REVERT: B 454 MET cc_start: 0.8340 (ttm) cc_final: 0.7828 (ttt) REVERT: B 536 ARG cc_start: 0.6516 (mtp180) cc_final: 0.6175 (mtm180) REVERT: B 551 LYS cc_start: 0.8850 (mttt) cc_final: 0.8448 (mptt) outliers start: 36 outliers final: 19 residues processed: 172 average time/residue: 0.0847 time to fit residues: 20.1830 Evaluate side-chains 162 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 423 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 105 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 208 GLN A 338 HIS ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.204499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.155569 restraints weight = 10475.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155585 restraints weight = 7987.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158152 restraints weight = 7053.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.157873 restraints weight = 4797.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158361 restraints weight = 5151.522| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9078 Z= 0.136 Angle : 0.585 6.893 12302 Z= 0.306 Chirality : 0.041 0.166 1484 Planarity : 0.004 0.067 1536 Dihedral : 6.479 59.537 1250 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 3.70 % Allowed : 20.99 % Favored : 75.31 % 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: 0.21 (0.25), residues: 1150 helix: 0.99 (0.20), residues: 742 sheet: -0.64 (0.68), residues: 66 loop : -1.52 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 345 TYR 0.010 0.001 TYR A 570 PHE 0.037 0.002 PHE B 31 TRP 0.005 0.001 TRP B 164 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 9078) covalent geometry : angle 0.58490 / 0.31 (12302) hydrogen bonds : bond 0.03651 / 2.42 ( 559) hydrogen bonds : angle 4.50859 / 3.17 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.208 Fit side-chains REVERT: A 127 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7633 (m) REVERT: A 238 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7199 (mtpt) REVERT: A 243 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 315 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 368 LYS cc_start: 0.8398 (mttm) cc_final: 0.8075 (mttm) REVERT: A 453 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 454 MET cc_start: 0.8144 (ttm) cc_final: 0.7655 (ttm) REVERT: A 551 LYS cc_start: 0.8814 (mttt) cc_final: 0.8360 (mptt) REVERT: B 80 LEU cc_start: 0.8777 (tp) cc_final: 0.8525 (tp) REVERT: B 127 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7646 (m) REVERT: B 243 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 299 GLN cc_start: 0.7449 (mm110) cc_final: 0.7249 (mm-40) REVERT: B 453 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 512 GLN cc_start: 0.7629 (tt0) cc_final: 0.7400 (tt0) REVERT: B 536 ARG cc_start: 0.6504 (mtp180) cc_final: 0.6295 (mtm-85) REVERT: B 551 LYS cc_start: 0.8846 (mttt) cc_final: 0.8448 (mptt) outliers start: 36 outliers final: 22 residues processed: 163 average time/residue: 0.0852 time to fit residues: 19.1484 Evaluate side-chains 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 577 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A 338 HIS B 208 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.198082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148385 restraints weight = 10605.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145517 restraints weight = 8930.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.148401 restraints weight = 8311.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149117 restraints weight = 5503.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149584 restraints weight = 5186.879| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9078 Z= 0.242 Angle : 0.669 6.354 12302 Z= 0.350 Chirality : 0.045 0.158 1484 Planarity : 0.005 0.068 1536 Dihedral : 6.527 59.678 1249 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 3.81 % Allowed : 22.12 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1150 helix: 0.91 (0.20), residues: 734 sheet: -0.69 (0.68), residues: 66 loop : -1.38 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 345 TYR 0.015 0.002 TYR A 83 PHE 0.032 0.002 PHE A 31 TRP 0.004 0.001 TRP A 104 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 ( 9078) covalent geometry : angle 0.66854 / 0.35 (12302) hydrogen bonds : bond 0.04040 / 2.71 ( 559) hydrogen bonds : angle 4.70845 / 3.31 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.230 Fit side-chains REVERT: A 118 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8331 (t0) REVERT: A 127 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7745 (m) REVERT: A 238 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7256 (mtpt) REVERT: A 243 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 315 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 453 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 551 LYS cc_start: 0.8866 (mttt) cc_final: 0.8373 (mptt) REVERT: B 80 LEU cc_start: 0.8808 (tp) cc_final: 0.8539 (tp) REVERT: B 127 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7788 (p) REVERT: B 243 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 368 LYS cc_start: 0.8529 (mttm) cc_final: 0.8200 (mttm) REVERT: B 453 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 454 MET cc_start: 0.8315 (ttm) cc_final: 0.7842 (ttt) REVERT: B 551 LYS cc_start: 0.8888 (mttt) cc_final: 0.8442 (mptt) REVERT: B 571 ARG cc_start: 0.7416 (ttm110) cc_final: 0.7202 (ttm-80) outliers start: 37 outliers final: 23 residues processed: 164 average time/residue: 0.0829 time to fit residues: 18.7921 Evaluate side-chains 156 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 0.0670 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 208 GLN A 338 HIS B 91 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.203801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153116 restraints weight = 10499.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.155430 restraints weight = 7001.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.157059 restraints weight = 5596.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157242 restraints weight = 4118.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157408 restraints weight = 3985.492| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9078 Z= 0.133 Angle : 0.588 7.285 12302 Z= 0.307 Chirality : 0.041 0.179 1484 Planarity : 0.004 0.066 1536 Dihedral : 6.336 58.972 1249 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 3.09 % Allowed : 23.46 % Favored : 73.46 % 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: 0.42 (0.26), residues: 1150 helix: 1.09 (0.20), residues: 744 sheet: -0.63 (0.69), residues: 66 loop : -1.29 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 345 TYR 0.009 0.001 TYR A 419 PHE 0.034 0.002 PHE A 31 TRP 0.005 0.001 TRP A 164 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9078) covalent geometry : angle 0.58755 / 0.31 (12302) hydrogen bonds : bond 0.03563 / 2.37 ( 559) hydrogen bonds : angle 4.43040 / 3.11 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.334 Fit side-chains REVERT: A 127 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7771 (m) REVERT: A 188 MET cc_start: 0.8322 (mmm) cc_final: 0.7655 (tpt) REVERT: A 238 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7255 (mtpt) REVERT: A 243 GLU cc_start: 0.7709 (tm-30) cc_final: 0.6682 (tm-30) REVERT: A 368 LYS cc_start: 0.8366 (mttm) cc_final: 0.8157 (mttm) REVERT: A 453 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 454 MET cc_start: 0.8059 (ttm) cc_final: 0.7781 (ttm) REVERT: A 551 LYS cc_start: 0.8816 (mttt) cc_final: 0.8384 (mptt) REVERT: B 80 LEU cc_start: 0.8737 (tp) cc_final: 0.8473 (tp) REVERT: B 118 ASN cc_start: 0.8620 (t0) cc_final: 0.8402 (t0) REVERT: B 127 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7712 (m) REVERT: B 243 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 299 GLN cc_start: 0.7493 (mm110) cc_final: 0.7274 (mm-40) REVERT: B 368 LYS cc_start: 0.8532 (mttm) cc_final: 0.8133 (mttm) REVERT: B 453 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 454 MET cc_start: 0.8269 (ttm) cc_final: 0.7799 (ttt) REVERT: B 512 GLN cc_start: 0.7719 (tt0) cc_final: 0.7470 (tt0) REVERT: B 551 LYS cc_start: 0.8765 (mttt) cc_final: 0.8405 (mptt) outliers start: 30 outliers final: 20 residues processed: 156 average time/residue: 0.0869 time to fit residues: 18.9849 Evaluate side-chains 151 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS A 535 HIS A 577 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.192964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142494 restraints weight = 10620.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139859 restraints weight = 8716.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142941 restraints weight = 8242.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142827 restraints weight = 5525.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143533 restraints weight = 5580.076| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 9078 Z= 0.360 Angle : 0.794 7.781 12302 Z= 0.414 Chirality : 0.049 0.227 1484 Planarity : 0.005 0.068 1536 Dihedral : 6.697 59.956 1249 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.35 % Rotamer: Outliers : 3.70 % Allowed : 22.74 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.15 (0.25), residues: 1150 helix: 0.69 (0.20), residues: 730 sheet: -0.77 (0.77), residues: 52 loop : -1.52 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 126 TYR 0.022 0.002 TYR A 83 PHE 0.036 0.002 PHE A 31 TRP 0.010 0.002 TRP B 104 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.36 ( 9078) covalent geometry : angle 0.79423 / 0.41 (12302) hydrogen bonds : bond 0.04442 / 2.99 ( 559) hydrogen bonds : angle 4.97545 / 3.50 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.351 Fit side-chains REVERT: A 127 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7505 (t) REVERT: A 238 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7503 (mtpt) REVERT: A 243 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 525 MET cc_start: 0.8636 (mmt) cc_final: 0.8061 (mmt) REVERT: A 536 ARG cc_start: 0.7267 (ptp-170) cc_final: 0.7061 (ptp-170) REVERT: A 551 LYS cc_start: 0.8908 (mttt) cc_final: 0.8452 (mptt) REVERT: B 80 LEU cc_start: 0.8819 (tp) cc_final: 0.8546 (tp) REVERT: B 127 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7780 (p) REVERT: B 205 LEU cc_start: 0.8268 (tt) cc_final: 0.7936 (tp) REVERT: B 243 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 368 LYS cc_start: 0.8503 (mttm) cc_final: 0.8172 (mttm) REVERT: B 453 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 551 LYS cc_start: 0.8876 (mttt) cc_final: 0.8499 (mptt) outliers start: 36 outliers final: 25 residues processed: 164 average time/residue: 0.0929 time to fit residues: 21.5961 Evaluate side-chains 160 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 84 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 208 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.201305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152439 restraints weight = 10459.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152332 restraints weight = 7717.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154733 restraints weight = 7027.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154746 restraints weight = 4819.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155067 restraints weight = 4996.522| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9078 Z= 0.143 Angle : 0.623 7.678 12302 Z= 0.324 Chirality : 0.042 0.247 1484 Planarity : 0.004 0.066 1536 Dihedral : 6.329 57.534 1249 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 2.78 % Allowed : 24.07 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.35 (0.26), residues: 1150 helix: 1.07 (0.20), residues: 742 sheet: -0.79 (0.68), residues: 66 loop : -1.35 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 345 TYR 0.011 0.001 TYR B 83 PHE 0.042 0.002 PHE A 31 TRP 0.005 0.001 TRP B 104 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9078) covalent geometry : angle 0.62280 / 0.32 (12302) hydrogen bonds : bond 0.03613 / 2.40 ( 559) hydrogen bonds : angle 4.51300 / 3.17 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.289 Fit side-chains REVERT: A 127 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7874 (m) REVERT: A 238 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7437 (mtpt) REVERT: A 243 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7504 (tm-30) REVERT: A 333 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7870 (mt0) REVERT: A 551 LYS cc_start: 0.8812 (mttt) cc_final: 0.8416 (mptt) REVERT: B 80 LEU cc_start: 0.8788 (tp) cc_final: 0.8526 (tp) REVERT: B 127 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7595 (m) REVERT: B 243 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 299 GLN cc_start: 0.7509 (mm110) cc_final: 0.7301 (mm-40) REVERT: B 368 LYS cc_start: 0.8501 (mttm) cc_final: 0.8169 (mttm) REVERT: B 453 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 454 MET cc_start: 0.8261 (ttm) cc_final: 0.8018 (ttt) REVERT: B 551 LYS cc_start: 0.8769 (mttt) cc_final: 0.8492 (mmmt) outliers start: 27 outliers final: 21 residues processed: 147 average time/residue: 0.0891 time to fit residues: 18.3897 Evaluate side-chains 149 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 0.0870 chunk 51 optimal weight: 0.3980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.205540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155908 restraints weight = 10442.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156914 restraints weight = 7439.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158642 restraints weight = 5882.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159063 restraints weight = 4975.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159260 restraints weight = 4510.537| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9078 Z= 0.127 Angle : 0.609 9.162 12302 Z= 0.313 Chirality : 0.041 0.266 1484 Planarity : 0.004 0.066 1536 Dihedral : 6.039 55.697 1249 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.88 % Allowed : 24.18 % Favored : 72.94 % 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: 0.62 (0.26), residues: 1150 helix: 1.28 (0.20), residues: 742 sheet: -0.69 (0.68), residues: 66 loop : -1.24 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 345 TYR 0.009 0.001 TYR B 83 PHE 0.021 0.001 PHE A 573 TRP 0.005 0.001 TRP A 104 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9078) covalent geometry : angle 0.60895 / 0.31 (12302) hydrogen bonds : bond 0.03410 / 2.24 ( 559) hydrogen bonds : angle 4.30078 / 3.01 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1324.08 seconds wall clock time: 23 minutes 35.97 seconds (1415.97 seconds total)