Starting phenix.real_space_refine on Thu Jul 31 00:52:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlp_22376/07_2025/7jlp_22376.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlp_22376/07_2025/7jlp_22376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2025/7jlp_22376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2025/7jlp_22376.map" model { file = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2025/7jlp_22376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlp_22376/07_2025/7jlp_22376.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 69 5.16 5 C 8643 2.51 5 N 2034 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12891 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "C" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 9, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 9, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 9, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 8.22, per 1000 atoms: 0.64 Number of scatterers: 12891 At special positions: 0 Unit cell: (128.142, 123.606, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 12 15.00 O 2133 8.00 N 2034 7.00 C 8643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 9 sheets defined 72.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.502A pdb=" N HIS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.042A pdb=" N ALA A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 132 through 166 removed outlier: 3.784A pdb=" N ILE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.560A pdb=" N THR A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.526A pdb=" N ASN A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.785A pdb=" N ARG A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 276 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 317 Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.618A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.678A pdb=" N CYS A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 3.739A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 398 removed outlier: 3.694A pdb=" N VAL A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 406 removed outlier: 5.969A pdb=" N GLU A 405 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 406 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.618A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.706A pdb=" N ARG A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 481 through 493 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 508 removed outlier: 3.640A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.502A pdb=" N HIS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.041A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 132 through 166 removed outlier: 3.784A pdb=" N ILE B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.560A pdb=" N THR B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 213 through 225 removed outlier: 3.527A pdb=" N ASN B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.784A pdb=" N ARG B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 276 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY B 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 317 Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.618A pdb=" N LEU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.677A pdb=" N CYS B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 3.739A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 398 removed outlier: 3.695A pdb=" N VAL B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 406 removed outlier: 5.969A pdb=" N GLU B 405 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS B 406 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.619A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 removed outlier: 3.706A pdb=" N ARG B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 481 through 493 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 508 removed outlier: 3.640A pdb=" N ILE B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.502A pdb=" N HIS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 86 Processing helix chain 'C' and resid 111 through 116 removed outlier: 4.041A pdb=" N ALA C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 116' Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 132 through 166 removed outlier: 3.784A pdb=" N ILE C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.560A pdb=" N THR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.527A pdb=" N ASN C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.784A pdb=" N ARG C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY C 276 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 277 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 317 Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.618A pdb=" N LEU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.677A pdb=" N CYS C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.739A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 Processing helix chain 'C' and resid 370 through 398 removed outlier: 3.695A pdb=" N VAL C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 406 removed outlier: 5.969A pdb=" N GLU C 405 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS C 406 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 422 Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.618A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 removed outlier: 3.706A pdb=" N ARG C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 481 through 493 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.641A pdb=" N ILE C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512 Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512 Processing sheet with id=AA7, first strand: chain 'C' and resid 231 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 331 through 332 Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512 693 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3735 1.34 - 1.46: 2104 1.46 - 1.58: 7226 1.58 - 1.69: 12 1.69 - 1.81: 105 Bond restraints: 13182 Sorted by residual: bond pdb=" C29 POV B 615 " pdb="C210 POV B 615 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C29 POV C 602 " pdb="C210 POV C 602 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV C 612 " pdb="C210 POV C 612 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV B 610 " pdb="C210 POV B 610 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV A 615 " pdb="C210 POV A 615 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 ... (remaining 13177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 17315 3.60 - 7.20: 283 7.20 - 10.81: 33 10.81 - 14.41: 3 14.41 - 18.01: 36 Bond angle restraints: 17670 Sorted by residual: angle pdb=" C28 POV B 605 " pdb=" C29 POV B 605 " pdb="C210 POV B 605 " ideal model delta sigma weight residual 127.79 109.78 18.01 3.00e+00 1.11e-01 3.60e+01 angle pdb=" C28 POV C 607 " pdb=" C29 POV C 607 " pdb="C210 POV C 607 " ideal model delta sigma weight residual 127.79 109.81 17.98 3.00e+00 1.11e-01 3.59e+01 angle pdb=" C28 POV A 605 " pdb=" C29 POV A 605 " pdb="C210 POV A 605 " ideal model delta sigma weight residual 127.79 109.84 17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" C28 POV C 613 " pdb=" C29 POV C 613 " pdb="C210 POV C 613 " ideal model delta sigma weight residual 127.79 109.91 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C28 POV A 611 " pdb=" C29 POV A 611 " pdb="C210 POV A 611 " ideal model delta sigma weight residual 127.79 109.92 17.87 3.00e+00 1.11e-01 3.55e+01 ... (remaining 17665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.36: 6849 18.36 - 36.73: 726 36.73 - 55.09: 198 55.09 - 73.46: 48 73.46 - 91.82: 42 Dihedral angle restraints: 7863 sinusoidal: 3585 harmonic: 4278 Sorted by residual: dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.29 35.29 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 122 " pdb=" CB CYS B 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.29 35.29 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 122 " pdb=" CB CYS C 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.28 35.28 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 7860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1050 0.028 - 0.055: 554 0.055 - 0.083: 199 0.083 - 0.111: 69 0.111 - 0.138: 6 Chirality restraints: 1878 Sorted by residual: chirality pdb=" CA ILE A 425 " pdb=" N ILE A 425 " pdb=" C ILE A 425 " pdb=" CB ILE A 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE C 425 " pdb=" N ILE C 425 " pdb=" C ILE C 425 " pdb=" CB ILE C 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE B 425 " pdb=" N ILE B 425 " pdb=" C ILE B 425 " pdb=" CB ILE B 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1875 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 605 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.07e+02 pdb=" C29 POV B 605 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV B 605 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV B 605 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 607 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.07e+02 pdb=" C29 POV C 607 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV C 607 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV C 607 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 605 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.06e+02 pdb=" C29 POV A 605 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV A 605 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV A 605 " 0.162 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2760 2.78 - 3.31: 11275 3.31 - 3.84: 19746 3.84 - 4.37: 23908 4.37 - 4.90: 42034 Nonbonded interactions: 99723 Sorted by model distance: nonbonded pdb=" NH2 ARG C 337 " pdb=" OE1 GLN C 351 " model vdw 2.252 3.120 nonbonded pdb=" NH2 ARG B 337 " pdb=" OE1 GLN B 351 " model vdw 2.252 3.120 nonbonded pdb=" NH2 ARG A 337 " pdb=" OE1 GLN A 351 " model vdw 2.252 3.120 nonbonded pdb=" O HIS A 406 " pdb=" OG1 THR A 410 " model vdw 2.273 3.040 nonbonded pdb=" O HIS C 406 " pdb=" OG1 THR C 410 " model vdw 2.273 3.040 ... (remaining 99718 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 through 532 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C310 or name C311 or name C312 or name C313 or name C314)) \ or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or resid 611 or (resid 613 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215)) or resid 615)) selection = (chain 'B' and (resid 36 through 532 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C310 or name C311 or name C312 or name C313 or name C314)) \ or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or resid 611 or (resid 613 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215)) or resid 615)) selection = (chain 'C' and (resid 36 through 532 or (resid 603 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 60 \ 4 or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or (resid 611 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or name C212 or name C213 or n \ ame C214 or name C215)) or resid 613 or (resid 615 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or name C212 or name C213 or \ name C214 or name C215 or name C216)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.620 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.009 0.189 13185 Z= 0.450 Angle : 1.270 18.010 17676 Z= 0.493 Chirality : 0.038 0.138 1878 Planarity : 0.018 0.301 2154 Dihedral : 17.666 91.820 5082 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.70 % Allowed : 2.09 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.21), residues: 1443 helix: -0.55 (0.16), residues: 957 sheet: -1.93 (0.89), residues: 30 loop : -3.02 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 180 HIS 0.004 0.001 HIS A 161 PHE 0.014 0.001 PHE A 163 TYR 0.005 0.001 TYR C 177 ARG 0.002 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.14722 ( 693) hydrogen bonds : angle 5.84978 ( 1980) SS BOND : bond 0.00133 ( 3) SS BOND : angle 0.57835 ( 6) covalent geometry : bond 0.00905 (13182) covalent geometry : angle 1.27066 (17670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.303 Fit side-chains REVERT: B 62 MET cc_start: 0.7912 (ttp) cc_final: 0.7626 (ttp) REVERT: B 91 ILE cc_start: 0.8718 (pt) cc_final: 0.8516 (pt) REVERT: B 191 GLN cc_start: 0.8041 (pp30) cc_final: 0.7740 (pp30) REVERT: B 306 ILE cc_start: 0.8944 (mt) cc_final: 0.8709 (mt) REVERT: B 524 MET cc_start: 0.4129 (ptp) cc_final: 0.3515 (ptp) REVERT: C 91 ILE cc_start: 0.8666 (pt) cc_final: 0.8438 (pt) REVERT: C 121 VAL cc_start: 0.7418 (p) cc_final: 0.7156 (t) outliers start: 9 outliers final: 7 residues processed: 168 average time/residue: 0.2782 time to fit residues: 65.5186 Evaluate side-chains 130 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 406 HIS A 428 GLN B 184 GLN B 250 ASN B 406 HIS B 507 ASN C 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.090497 restraints weight = 15932.092| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.31 r_work: 0.2642 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13185 Z= 0.120 Angle : 0.461 6.041 17676 Z= 0.237 Chirality : 0.037 0.137 1878 Planarity : 0.004 0.040 2154 Dihedral : 15.787 84.968 2287 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.70 % Allowed : 6.81 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1443 helix: 0.99 (0.17), residues: 942 sheet: -1.72 (0.91), residues: 30 loop : -2.56 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 292 HIS 0.004 0.001 HIS B 342 PHE 0.012 0.001 PHE C 469 TYR 0.013 0.001 TYR A 152 ARG 0.007 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 693) hydrogen bonds : angle 3.95696 ( 1980) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.35899 ( 6) covalent geometry : bond 0.00275 (13182) covalent geometry : angle 0.46129 (17670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 1.314 Fit side-chains REVERT: A 159 GLU cc_start: 0.8410 (tt0) cc_final: 0.8135 (tt0) REVERT: A 233 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7597 (tpp80) REVERT: A 245 ARG cc_start: 0.8407 (mtt-85) cc_final: 0.7882 (mtm110) REVERT: A 524 MET cc_start: 0.5067 (ptp) cc_final: 0.3498 (ptm) REVERT: B 62 MET cc_start: 0.8477 (ttp) cc_final: 0.8152 (ttp) REVERT: B 91 ILE cc_start: 0.8828 (pt) cc_final: 0.8616 (pt) REVERT: B 191 GLN cc_start: 0.8298 (pp30) cc_final: 0.8004 (pt0) REVERT: B 306 ILE cc_start: 0.9017 (mt) cc_final: 0.8743 (mt) REVERT: B 375 LEU cc_start: 0.8914 (mt) cc_final: 0.8652 (mt) REVERT: B 524 MET cc_start: 0.4634 (ptp) cc_final: 0.3801 (ptp) outliers start: 9 outliers final: 9 residues processed: 137 average time/residue: 0.2695 time to fit residues: 52.3010 Evaluate side-chains 121 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN A 379 ASN B 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.110660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.089565 restraints weight = 16099.607| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.31 r_work: 0.2628 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13185 Z= 0.135 Angle : 0.455 5.267 17676 Z= 0.233 Chirality : 0.038 0.133 1878 Planarity : 0.003 0.029 2154 Dihedral : 15.161 88.880 2277 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.77 % Allowed : 8.82 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1443 helix: 1.54 (0.17), residues: 942 sheet: -2.83 (0.63), residues: 60 loop : -2.25 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 180 HIS 0.004 0.001 HIS A 161 PHE 0.013 0.001 PHE A 469 TYR 0.013 0.001 TYR A 152 ARG 0.006 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 693) hydrogen bonds : angle 3.81836 ( 1980) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.30446 ( 6) covalent geometry : bond 0.00321 (13182) covalent geometry : angle 0.45554 (17670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.379 Fit side-chains REVERT: A 159 GLU cc_start: 0.8348 (tt0) cc_final: 0.7976 (tt0) REVERT: A 233 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7545 (tpp80) REVERT: A 245 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.7940 (mtm110) REVERT: A 524 MET cc_start: 0.5031 (ptp) cc_final: 0.3414 (ptm) REVERT: B 62 MET cc_start: 0.8486 (ttp) cc_final: 0.8147 (ttp) REVERT: B 91 ILE cc_start: 0.8835 (pt) cc_final: 0.8600 (pt) REVERT: B 191 GLN cc_start: 0.8241 (pp30) cc_final: 0.7960 (pt0) REVERT: B 306 ILE cc_start: 0.9049 (mt) cc_final: 0.8781 (mt) REVERT: B 375 LEU cc_start: 0.8878 (mt) cc_final: 0.8632 (mt) REVERT: B 524 MET cc_start: 0.4585 (ptp) cc_final: 0.3713 (ptp) outliers start: 10 outliers final: 9 residues processed: 131 average time/residue: 0.2826 time to fit residues: 52.6978 Evaluate side-chains 122 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 95 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN B 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.113295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.092420 restraints weight = 15824.805| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.31 r_work: 0.2671 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13185 Z= 0.093 Angle : 0.413 5.545 17676 Z= 0.214 Chirality : 0.036 0.133 1878 Planarity : 0.003 0.029 2154 Dihedral : 14.279 89.268 2277 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.93 % Allowed : 9.44 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1443 helix: 1.95 (0.18), residues: 933 sheet: -1.28 (0.91), residues: 30 loop : -1.93 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.003 0.000 HIS B 161 PHE 0.009 0.001 PHE B 469 TYR 0.013 0.001 TYR A 152 ARG 0.005 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 693) hydrogen bonds : angle 3.62781 ( 1980) SS BOND : bond 0.00098 ( 3) SS BOND : angle 0.26596 ( 6) covalent geometry : bond 0.00201 (13182) covalent geometry : angle 0.41297 (17670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.348 Fit side-chains REVERT: A 159 GLU cc_start: 0.8276 (tt0) cc_final: 0.7909 (tt0) REVERT: A 233 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7510 (tpp80) REVERT: A 245 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.7940 (mtm110) REVERT: A 524 MET cc_start: 0.4878 (ptp) cc_final: 0.3357 (ptm) REVERT: B 191 GLN cc_start: 0.8236 (pp30) cc_final: 0.7921 (pt0) REVERT: B 306 ILE cc_start: 0.9013 (mt) cc_final: 0.8722 (mt) REVERT: B 428 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8237 (mt0) REVERT: B 477 LEU cc_start: 0.8899 (tp) cc_final: 0.8430 (mp) REVERT: B 479 GLU cc_start: 0.8722 (tp30) cc_final: 0.8468 (tp30) REVERT: B 524 MET cc_start: 0.4553 (ptp) cc_final: 0.3705 (ptp) REVERT: C 524 MET cc_start: 0.5054 (ptp) cc_final: 0.3726 (ptm) outliers start: 12 outliers final: 9 residues processed: 138 average time/residue: 0.2705 time to fit residues: 53.3607 Evaluate side-chains 127 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 0.0470 chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 184 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.111997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.091023 restraints weight = 15987.857| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.31 r_work: 0.2651 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13185 Z= 0.117 Angle : 0.437 6.080 17676 Z= 0.223 Chirality : 0.037 0.132 1878 Planarity : 0.003 0.027 2154 Dihedral : 13.979 88.940 2277 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.93 % Allowed : 10.44 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1443 helix: 2.23 (0.18), residues: 921 sheet: -1.18 (0.92), residues: 30 loop : -1.62 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 180 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE A 469 TYR 0.013 0.001 TYR A 152 ARG 0.006 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 693) hydrogen bonds : angle 3.64086 ( 1980) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.21992 ( 6) covalent geometry : bond 0.00273 (13182) covalent geometry : angle 0.43680 (17670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.467 Fit side-chains REVERT: A 125 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7426 (mtp180) REVERT: A 159 GLU cc_start: 0.8322 (tt0) cc_final: 0.7934 (tt0) REVERT: A 233 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7531 (tpp80) REVERT: A 245 ARG cc_start: 0.8497 (mtt-85) cc_final: 0.7966 (mtm110) REVERT: B 191 GLN cc_start: 0.8161 (pp30) cc_final: 0.7826 (pt0) REVERT: B 306 ILE cc_start: 0.9032 (mt) cc_final: 0.8712 (mt) REVERT: B 428 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8254 (mt0) REVERT: B 477 LEU cc_start: 0.8903 (tp) cc_final: 0.8425 (mp) REVERT: B 479 GLU cc_start: 0.8725 (tp30) cc_final: 0.8451 (tp30) REVERT: B 524 MET cc_start: 0.4431 (ptp) cc_final: 0.3511 (ptp) REVERT: C 428 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8097 (mt0) REVERT: C 460 GLN cc_start: 0.8601 (tt0) cc_final: 0.8148 (pt0) REVERT: C 524 MET cc_start: 0.4762 (ptp) cc_final: 0.3767 (ptm) outliers start: 12 outliers final: 11 residues processed: 138 average time/residue: 0.2679 time to fit residues: 53.5972 Evaluate side-chains 134 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.109013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.087764 restraints weight = 16361.292| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 1.33 r_work: 0.2599 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13185 Z= 0.193 Angle : 0.505 6.735 17676 Z= 0.255 Chirality : 0.040 0.133 1878 Planarity : 0.003 0.030 2154 Dihedral : 14.492 88.565 2277 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.39 % Allowed : 10.44 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1443 helix: 1.98 (0.17), residues: 939 sheet: -1.18 (0.92), residues: 30 loop : -1.50 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 180 HIS 0.005 0.001 HIS B 348 PHE 0.011 0.001 PHE C 469 TYR 0.012 0.001 TYR B 209 ARG 0.005 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 693) hydrogen bonds : angle 3.82687 ( 1980) SS BOND : bond 0.00331 ( 3) SS BOND : angle 0.24297 ( 6) covalent geometry : bond 0.00476 (13182) covalent geometry : angle 0.50550 (17670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.437 Fit side-chains REVERT: A 159 GLU cc_start: 0.8355 (tt0) cc_final: 0.8013 (tt0) REVERT: A 233 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7539 (tpp80) REVERT: A 524 MET cc_start: 0.5044 (ptp) cc_final: 0.3477 (ptm) REVERT: B 191 GLN cc_start: 0.8181 (pp30) cc_final: 0.7910 (pt0) REVERT: B 245 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7919 (mtp85) REVERT: B 306 ILE cc_start: 0.9034 (mt) cc_final: 0.8734 (mt) REVERT: B 524 MET cc_start: 0.4541 (ptp) cc_final: 0.3554 (ptp) REVERT: C 91 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8489 (pt) REVERT: C 428 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8187 (mt0) REVERT: C 460 GLN cc_start: 0.8627 (tt0) cc_final: 0.8146 (pt0) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.2704 time to fit residues: 50.9570 Evaluate side-chains 131 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.111065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.090057 restraints weight = 15942.191| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.31 r_work: 0.2633 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13185 Z= 0.125 Angle : 0.451 5.631 17676 Z= 0.230 Chirality : 0.038 0.134 1878 Planarity : 0.003 0.028 2154 Dihedral : 13.998 87.187 2277 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.24 % Allowed : 11.14 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1443 helix: 2.29 (0.18), residues: 924 sheet: -1.10 (0.93), residues: 30 loop : -1.55 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS B 161 PHE 0.010 0.001 PHE A 469 TYR 0.011 0.001 TYR A 152 ARG 0.007 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 693) hydrogen bonds : angle 3.71262 ( 1980) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.25268 ( 6) covalent geometry : bond 0.00293 (13182) covalent geometry : angle 0.45153 (17670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.316 Fit side-chains REVERT: A 159 GLU cc_start: 0.8315 (tt0) cc_final: 0.7991 (tt0) REVERT: A 233 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7529 (tpp80) REVERT: A 245 ARG cc_start: 0.8525 (mtt-85) cc_final: 0.8093 (mtm110) REVERT: A 524 MET cc_start: 0.4995 (ptp) cc_final: 0.3455 (ptm) REVERT: B 191 GLN cc_start: 0.8127 (pp30) cc_final: 0.7809 (pt0) REVERT: B 306 ILE cc_start: 0.9043 (mt) cc_final: 0.8766 (mt) REVERT: B 428 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8317 (mt0) REVERT: B 479 GLU cc_start: 0.8737 (tp30) cc_final: 0.8417 (tp30) REVERT: B 524 MET cc_start: 0.4496 (ptp) cc_final: 0.3547 (ptp) REVERT: C 91 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8521 (pt) REVERT: C 428 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8159 (mt0) REVERT: C 460 GLN cc_start: 0.8626 (tt0) cc_final: 0.8158 (pt0) REVERT: C 524 MET cc_start: 0.4616 (ptp) cc_final: 0.3735 (ptm) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.2578 time to fit residues: 52.0887 Evaluate side-chains 136 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.112039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.091019 restraints weight = 15932.383| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.32 r_work: 0.2648 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13185 Z= 0.109 Angle : 0.439 7.266 17676 Z= 0.224 Chirality : 0.037 0.133 1878 Planarity : 0.003 0.029 2154 Dihedral : 13.467 84.727 2277 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.39 % Allowed : 11.45 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.23), residues: 1443 helix: 2.35 (0.18), residues: 933 sheet: -1.05 (0.93), residues: 30 loop : -1.41 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE A 469 TYR 0.010 0.001 TYR C 152 ARG 0.007 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 693) hydrogen bonds : angle 3.63629 ( 1980) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.20668 ( 6) covalent geometry : bond 0.00250 (13182) covalent geometry : angle 0.43867 (17670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.334 Fit side-chains REVERT: A 125 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7448 (mtp180) REVERT: A 159 GLU cc_start: 0.8340 (tt0) cc_final: 0.8015 (tt0) REVERT: A 233 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.7530 (tpp80) REVERT: A 245 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.8076 (mtm110) REVERT: A 524 MET cc_start: 0.4771 (ptp) cc_final: 0.3712 (ptp) REVERT: B 191 GLN cc_start: 0.8122 (pp30) cc_final: 0.7878 (pt0) REVERT: B 306 ILE cc_start: 0.9039 (mt) cc_final: 0.8747 (mt) REVERT: B 428 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8281 (mt0) REVERT: B 524 MET cc_start: 0.4559 (ptp) cc_final: 0.3651 (ptp) REVERT: C 91 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8443 (pt) REVERT: C 193 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.5847 (mp0) REVERT: C 428 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8189 (mt0) REVERT: C 460 GLN cc_start: 0.8599 (tt0) cc_final: 0.8111 (pt0) REVERT: C 524 MET cc_start: 0.4749 (ptp) cc_final: 0.3865 (ptm) outliers start: 18 outliers final: 14 residues processed: 140 average time/residue: 0.2720 time to fit residues: 54.6886 Evaluate side-chains 142 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 184 GLN A 278 GLN C 250 ASN C 507 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.108850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.087467 restraints weight = 16093.783| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.33 r_work: 0.2595 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13185 Z= 0.205 Angle : 0.528 7.118 17676 Z= 0.264 Chirality : 0.041 0.133 1878 Planarity : 0.003 0.030 2154 Dihedral : 14.229 85.580 2277 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.39 % Allowed : 12.14 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1443 helix: 2.12 (0.17), residues: 939 sheet: -1.06 (0.93), residues: 30 loop : -1.37 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 180 HIS 0.005 0.001 HIS B 348 PHE 0.010 0.001 PHE B 465 TYR 0.011 0.001 TYR B 209 ARG 0.006 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 693) hydrogen bonds : angle 3.82391 ( 1980) SS BOND : bond 0.00386 ( 3) SS BOND : angle 0.22186 ( 6) covalent geometry : bond 0.00506 (13182) covalent geometry : angle 0.52792 (17670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.545 Fit side-chains REVERT: A 159 GLU cc_start: 0.8332 (tt0) cc_final: 0.7967 (tt0) REVERT: A 233 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7534 (tpp80) REVERT: A 245 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8066 (mtm110) REVERT: B 191 GLN cc_start: 0.8146 (pp30) cc_final: 0.7799 (pt0) REVERT: B 306 ILE cc_start: 0.9036 (mt) cc_final: 0.8757 (mt) REVERT: C 193 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.5849 (mp0) REVERT: C 428 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8240 (mt0) REVERT: C 524 MET cc_start: 0.4716 (ptp) cc_final: 0.3869 (ptm) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.3051 time to fit residues: 59.3997 Evaluate side-chains 133 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN A 278 GLN C 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.111837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.090790 restraints weight = 15899.629| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.32 r_work: 0.2640 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13185 Z= 0.117 Angle : 0.451 6.633 17676 Z= 0.230 Chirality : 0.038 0.133 1878 Planarity : 0.003 0.028 2154 Dihedral : 13.603 84.433 2277 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.31 % Allowed : 12.37 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.23), residues: 1443 helix: 2.32 (0.18), residues: 933 sheet: -0.99 (0.94), residues: 30 loop : -1.38 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE A 469 TYR 0.011 0.001 TYR C 152 ARG 0.007 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 693) hydrogen bonds : angle 3.66557 ( 1980) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.25680 ( 6) covalent geometry : bond 0.00272 (13182) covalent geometry : angle 0.45144 (17670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.404 Fit side-chains REVERT: A 159 GLU cc_start: 0.8326 (tt0) cc_final: 0.8008 (tt0) REVERT: A 233 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7505 (tpp80) REVERT: A 245 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.8081 (mtm110) REVERT: A 524 MET cc_start: 0.4774 (ptp) cc_final: 0.3722 (ptp) REVERT: B 191 GLN cc_start: 0.8078 (pp30) cc_final: 0.7775 (pt0) REVERT: B 306 ILE cc_start: 0.9035 (mt) cc_final: 0.8758 (mt) REVERT: B 428 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8305 (mt0) REVERT: B 524 MET cc_start: 0.4578 (ptp) cc_final: 0.3076 (ptm) REVERT: C 193 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.5870 (mp0) REVERT: C 428 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8168 (mt0) REVERT: C 524 MET cc_start: 0.4704 (ptp) cc_final: 0.3834 (ptm) outliers start: 17 outliers final: 15 residues processed: 137 average time/residue: 0.2714 time to fit residues: 53.3335 Evaluate side-chains 140 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 143 optimal weight: 0.1980 chunk 133 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.112634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.091685 restraints weight = 15908.017| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.31 r_work: 0.2656 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13185 Z= 0.103 Angle : 0.435 6.425 17676 Z= 0.223 Chirality : 0.037 0.133 1878 Planarity : 0.003 0.029 2154 Dihedral : 13.082 82.165 2277 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.16 % Allowed : 12.68 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1443 helix: 2.46 (0.18), residues: 930 sheet: -0.95 (0.94), residues: 30 loop : -1.30 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.004 0.000 HIS B 161 PHE 0.009 0.001 PHE A 469 TYR 0.011 0.001 TYR C 152 ARG 0.007 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 693) hydrogen bonds : angle 3.58339 ( 1980) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.20970 ( 6) covalent geometry : bond 0.00235 (13182) covalent geometry : angle 0.43532 (17670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6152.01 seconds wall clock time: 106 minutes 59.70 seconds (6419.70 seconds total)