Starting phenix.real_space_refine on Fri Jul 3 08:37:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n6r_24209/07_2026/7n6r_24209.map" } resolution = 3.93 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= 0.005 sd= 1.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 8656 2.51 5 N 2004 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 12708 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "B" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "C" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "D" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3070 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 4 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.75, per 1000 atoms: 0.22 Number of scatterers: 12708 At special positions: 0 Unit cell: (112.455, 184.093, 74.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 1948 8.00 N 2004 7.00 C 8656 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: 0.97 Conformation dependent library (CDL) restraints added in 636.9 milliseconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 117 through 143 removed outlier: 3.647A pdb=" N ARG A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 162 through 189 Proline residue: A 172 - end of helix Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.805A pdb=" N ALA A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 226 through 255 removed outlier: 4.340A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.587A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.597A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.631A pdb=" N PHE A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.745A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.890A pdb=" N ARG A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.468A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.634A pdb=" N HIS A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.837A pdb=" N PHE A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 499 removed outlier: 4.171A pdb=" N MET A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 117 through 144 removed outlier: 3.638A pdb=" N ARG B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 162 through 189 Proline residue: B 172 - end of helix Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.821A pdb=" N ALA B 205 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 225 through 255 removed outlier: 4.039A pdb=" N LEU B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.591A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 293 through 318 Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.583A pdb=" N PHE B 323 " --> pdb=" O CYS B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.727A pdb=" N LEU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 406 through 415 removed outlier: 3.893A pdb=" N ARG B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 removed outlier: 4.456A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 442 removed outlier: 3.581A pdb=" N HIS B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 462 removed outlier: 3.814A pdb=" N PHE B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 499 removed outlier: 4.176A pdb=" N MET B 477 " --> pdb=" O TRP B 473 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 117 through 143 removed outlier: 3.652A pdb=" N ARG C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 162 through 189 Proline residue: C 172 - end of helix Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.803A pdb=" N ALA C 205 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 226 through 255 removed outlier: 4.319A pdb=" N LEU C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Proline residue: C 252 - end of helix removed outlier: 3.587A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.604A pdb=" N PHE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 318 Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.632A pdb=" N PHE C 323 " --> pdb=" O CYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.751A pdb=" N LEU C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 360 Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 406 through 415 removed outlier: 3.904A pdb=" N ARG C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 423 removed outlier: 4.469A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 442 removed outlier: 3.627A pdb=" N HIS C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 462 removed outlier: 3.834A pdb=" N PHE C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 499 removed outlier: 4.170A pdb=" N MET C 477 " --> pdb=" O TRP C 473 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR C 497 " --> pdb=" O CYS C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 117 through 144 removed outlier: 3.637A pdb=" N ARG D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 162 through 189 Proline residue: D 172 - end of helix Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.824A pdb=" N ALA D 205 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 225 through 255 removed outlier: 4.040A pdb=" N LEU D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Proline residue: D 252 - end of helix removed outlier: 3.591A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 293 through 318 Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.583A pdb=" N PHE D 323 " --> pdb=" O CYS D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.729A pdb=" N LEU D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 406 through 415 removed outlier: 3.895A pdb=" N ARG D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 423 removed outlier: 4.455A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.579A pdb=" N HIS D 434 " --> pdb=" O SER D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 462 removed outlier: 3.814A pdb=" N PHE D 462 " --> pdb=" O GLY D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 499 removed outlier: 4.175A pdb=" N MET D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN D 488 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 497 " --> pdb=" O CYS D 493 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2340 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: 1.76 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1976 1.33 - 1.45: 3818 1.45 - 1.57: 7154 1.57 - 1.69: 16 1.69 - 1.82: 156 Bond restraints: 13120 Sorted by residual: bond pdb=" C19 ROV D 601 " pdb=" C20 ROV D 601 " ideal model delta sigma weight residual 1.534 1.367 0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C19 ROV A 601 " pdb=" C20 ROV A 601 " ideal model delta sigma weight residual 1.534 1.367 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C19 ROV B 601 " pdb=" C20 ROV B 601 " ideal model delta sigma weight residual 1.534 1.368 0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C19 ROV C 601 " pdb=" C20 ROV C 601 " ideal model delta sigma weight residual 1.534 1.368 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C18 ROV C 601 " pdb=" C22 ROV C 601 " ideal model delta sigma weight residual 1.538 1.374 0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 11279 1.54 - 3.08: 4970 3.08 - 4.62: 1367 4.62 - 6.16: 225 6.16 - 7.70: 23 Bond angle restraints: 17864 Sorted by residual: angle pdb=" C GLY D 457 " pdb=" N GLY D 458 " pdb=" CA GLY D 458 " ideal model delta sigma weight residual 120.03 125.62 -5.59 1.12e+00 7.97e-01 2.49e+01 angle pdb=" C GLY B 457 " pdb=" N GLY B 458 " pdb=" CA GLY B 458 " ideal model delta sigma weight residual 120.03 125.60 -5.57 1.12e+00 7.97e-01 2.47e+01 angle pdb=" C GLY A 457 " pdb=" N GLY A 458 " pdb=" CA GLY A 458 " ideal model delta sigma weight residual 120.03 125.60 -5.57 1.12e+00 7.97e-01 2.47e+01 angle pdb=" C GLY C 457 " pdb=" N GLY C 458 " pdb=" CA GLY C 458 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.46e+01 angle pdb=" C LEU A 199 " pdb=" N GLY A 200 " pdb=" CA GLY A 200 " ideal model delta sigma weight residual 120.03 125.12 -5.09 1.12e+00 7.97e-01 2.07e+01 ... (remaining 17859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6529 17.71 - 35.41: 633 35.41 - 53.12: 154 53.12 - 70.83: 34 70.83 - 88.53: 18 Dihedral angle restraints: 7368 sinusoidal: 2960 harmonic: 4408 Sorted by residual: dihedral pdb=" CA VAL D 117 " pdb=" C VAL D 117 " pdb=" N GLN D 118 " pdb=" CA GLN D 118 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA VAL C 117 " pdb=" C VAL C 117 " pdb=" N GLN C 118 " pdb=" CA GLN C 118 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL B 117 " pdb=" C VAL B 117 " pdb=" N GLN B 118 " pdb=" CA GLN B 118 " ideal model delta harmonic sigma weight residual 180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1009 0.058 - 0.116: 715 0.116 - 0.173: 233 0.173 - 0.231: 15 0.231 - 0.289: 12 Chirality restraints: 1984 Sorted by residual: chirality pdb=" C13 CLR A 603 " pdb=" C12 CLR A 603 " pdb=" C14 CLR A 603 " pdb=" C17 CLR A 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C13 CLR D 602 " pdb=" C12 CLR D 602 " pdb=" C14 CLR D 602 " pdb=" C17 CLR D 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C13 CLR B 603 " pdb=" C12 CLR B 603 " pdb=" C14 CLR B 603 " pdb=" C17 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1981 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 490 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C SER A 490 " -0.035 2.00e-02 2.50e+03 pdb=" O SER A 490 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 491 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 490 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C SER C 490 " 0.035 2.00e-02 2.50e+03 pdb=" O SER C 490 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU C 491 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 490 " -0.009 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C SER B 490 " 0.034 2.00e-02 2.50e+03 pdb=" O SER B 490 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 491 " -0.012 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1339 2.79 - 3.32: 13402 3.32 - 3.85: 19526 3.85 - 4.37: 24118 4.37 - 4.90: 40058 Nonbonded interactions: 98443 Sorted by model distance: nonbonded pdb=" O ILE C 281 " pdb=" OH TYR C 286 " model vdw 2.264 3.040 nonbonded pdb=" O ILE A 281 " pdb=" OH TYR A 286 " model vdw 2.264 3.040 nonbonded pdb=" O ILE D 281 " pdb=" OH TYR D 286 " model vdw 2.282 3.040 nonbonded pdb=" O ILE B 281 " pdb=" OH TYR B 286 " model vdw 2.283 3.040 nonbonded pdb=" NE2 GLN D 236 " pdb=" OH TYR D 436 " model vdw 2.395 3.120 ... (remaining 98438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.120 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.015 0.167 13120 Z= 1.093 Angle : 1.794 7.702 17864 Z= 1.333 Chirality : 0.078 0.289 1984 Planarity : 0.004 0.020 2108 Dihedral : 15.797 88.533 4520 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.14 % Favored : 94.59 % Rotamer: Outliers : 1.24 % Allowed : 8.20 % Favored : 90.56 % 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: -3.93 (0.18), residues: 1460 helix: -2.25 (0.13), residues: 1044 sheet: None (None), residues: 0 loop : -3.07 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 392 TYR 0.020 0.003 TYR A 271 PHE 0.028 0.003 PHE C 444 TRP 0.019 0.002 TRP C 401 HIS 0.008 0.002 HIS C 119 Details of bonding type rmsd/Z covalent geometry : bond 0.01517 / 1.09 (13120) covalent geometry : angle 1.79362 / 1.33 (17864) hydrogen bonds : bond 0.17050 / 10.83 ( 780) hydrogen bonds : angle 8.96107 / 6.37 ( 2340) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 393 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.8215 (mt0) cc_final: 0.7946 (mp10) REVERT: A 122 THR cc_start: 0.8837 (m) cc_final: 0.8574 (m) REVERT: A 135 ILE cc_start: 0.7723 (tt) cc_final: 0.7488 (tt) REVERT: A 284 GLU cc_start: 0.8456 (pp20) cc_final: 0.7832 (pt0) REVERT: A 374 ASP cc_start: 0.7715 (t0) cc_final: 0.7342 (t0) REVERT: A 442 LEU cc_start: 0.8203 (mt) cc_final: 0.7987 (mt) REVERT: A 444 PHE cc_start: 0.6957 (m-80) cc_final: 0.6523 (m-80) REVERT: A 480 MET cc_start: 0.7851 (mmt) cc_final: 0.7094 (tmm) REVERT: B 169 THR cc_start: 0.8313 (t) cc_final: 0.8077 (p) REVERT: B 170 TRP cc_start: 0.8127 (t60) cc_final: 0.7350 (t60) REVERT: B 247 LEU cc_start: 0.9193 (mm) cc_final: 0.8805 (tt) REVERT: B 274 PHE cc_start: 0.8400 (t80) cc_final: 0.8134 (t80) REVERT: B 350 MET cc_start: 0.7928 (mmm) cc_final: 0.6976 (tmm) REVERT: B 360 HIS cc_start: 0.8052 (t70) cc_final: 0.7311 (t70) REVERT: B 380 ASP cc_start: 0.7305 (p0) cc_final: 0.6611 (p0) REVERT: B 381 TRP cc_start: 0.9071 (p-90) cc_final: 0.8842 (p-90) REVERT: B 393 THR cc_start: 0.8673 (p) cc_final: 0.7810 (t) REVERT: B 419 ARG cc_start: 0.5983 (ptt-90) cc_final: 0.4807 (ptm160) REVERT: B 423 MET cc_start: 0.8165 (ttp) cc_final: 0.7944 (tpp) REVERT: B 435 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: B 473 TRP cc_start: 0.7827 (t-100) cc_final: 0.6694 (m-90) REVERT: C 115 MET cc_start: 0.8317 (tpt) cc_final: 0.8111 (tpt) REVERT: C 374 ASP cc_start: 0.7769 (t0) cc_final: 0.7198 (t0) REVERT: C 444 PHE cc_start: 0.7026 (m-80) cc_final: 0.6510 (m-80) REVERT: D 102 LYS cc_start: 0.7984 (tttm) cc_final: 0.7476 (tppt) REVERT: D 170 TRP cc_start: 0.8076 (t60) cc_final: 0.7051 (t60) REVERT: D 247 LEU cc_start: 0.9139 (mm) cc_final: 0.8730 (tt) REVERT: D 266 PRO cc_start: 0.7397 (Cg_endo) cc_final: 0.6564 (Cg_exo) REVERT: D 379 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7043 (mtp85) REVERT: D 380 ASP cc_start: 0.6825 (p0) cc_final: 0.6510 (p0) REVERT: D 391 TYR cc_start: 0.7876 (m-80) cc_final: 0.7487 (t80) REVERT: D 393 THR cc_start: 0.8475 (p) cc_final: 0.7616 (t) REVERT: D 428 LEU cc_start: 0.8825 (tp) cc_final: 0.8594 (pp) REVERT: D 435 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: D 473 TRP cc_start: 0.7937 (t-100) cc_final: 0.6625 (m-90) REVERT: D 476 LEU cc_start: 0.8259 (tt) cc_final: 0.7426 (mm) outliers start: 16 outliers final: 3 residues processed: 401 average time/residue: 0.0956 time to fit residues: 55.5313 Evaluate side-chains 273 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 268 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain D residue 435 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 236 GLN B 207 HIS B 217 HIS B 236 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN C 207 HIS C 236 GLN D 217 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122756 restraints weight = 22222.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125469 restraints weight = 12984.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127267 restraints weight = 9157.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128416 restraints weight = 7329.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.128808 restraints weight = 6384.695| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13120 Z= 0.146 Angle : 0.722 9.984 17864 Z= 0.345 Chirality : 0.041 0.137 1984 Planarity : 0.005 0.039 2108 Dihedral : 9.028 86.631 1822 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.87 % Allowed : 20.05 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1460 helix: -0.06 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 317 TYR 0.021 0.001 TYR D 391 PHE 0.015 0.001 PHE B 143 TRP 0.027 0.001 TRP D 188 HIS 0.004 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (13120) covalent geometry : angle 0.72157 / 0.34 (17864) hydrogen bonds : bond 0.04077 / 2.65 ( 780) hydrogen bonds : angle 5.16339 / 3.74 ( 2340) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8472 (tt) cc_final: 0.8230 (tt) REVERT: A 338 LEU cc_start: 0.7993 (tp) cc_final: 0.7773 (tp) REVERT: A 368 GLU cc_start: 0.8182 (tp30) cc_final: 0.7736 (tp30) REVERT: A 391 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6659 (t80) REVERT: A 442 LEU cc_start: 0.8597 (mt) cc_final: 0.8363 (mt) REVERT: A 444 PHE cc_start: 0.8236 (m-80) cc_final: 0.7625 (m-80) REVERT: B 247 LEU cc_start: 0.8648 (mm) cc_final: 0.8173 (tt) REVERT: B 281 ILE cc_start: 0.8690 (mm) cc_final: 0.8242 (tp) REVERT: B 300 ASN cc_start: 0.7631 (m-40) cc_final: 0.7108 (t0) REVERT: B 350 MET cc_start: 0.7792 (mmm) cc_final: 0.7392 (mpp) REVERT: B 366 PHE cc_start: 0.8937 (m-80) cc_final: 0.8654 (m-10) REVERT: B 380 ASP cc_start: 0.7071 (p0) cc_final: 0.6796 (p0) REVERT: B 393 THR cc_start: 0.8930 (p) cc_final: 0.8513 (t) REVERT: B 419 ARG cc_start: 0.5848 (ptt-90) cc_final: 0.4762 (ptm160) REVERT: B 473 TRP cc_start: 0.7637 (t-100) cc_final: 0.6988 (m-90) REVERT: C 188 TRP cc_start: 0.6396 (t-100) cc_final: 0.6100 (t-100) REVERT: C 223 GLN cc_start: 0.6571 (mt0) cc_final: 0.6360 (pp30) REVERT: C 368 GLU cc_start: 0.8136 (tp30) cc_final: 0.7860 (tp30) REVERT: C 391 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6846 (t80) REVERT: C 444 PHE cc_start: 0.8343 (m-80) cc_final: 0.7504 (m-80) REVERT: D 170 TRP cc_start: 0.8168 (t60) cc_final: 0.7596 (t60) REVERT: D 201 CYS cc_start: 0.6905 (m) cc_final: 0.6119 (p) REVERT: D 237 VAL cc_start: 0.8856 (m) cc_final: 0.8650 (p) REVERT: D 247 LEU cc_start: 0.8549 (mm) cc_final: 0.8113 (tt) REVERT: D 380 ASP cc_start: 0.6446 (p0) cc_final: 0.6040 (p0) REVERT: D 473 TRP cc_start: 0.7698 (t-100) cc_final: 0.7084 (m-90) REVERT: D 476 LEU cc_start: 0.8804 (tt) cc_final: 0.7780 (mm) outliers start: 50 outliers final: 22 residues processed: 348 average time/residue: 0.0844 time to fit residues: 44.6770 Evaluate side-chains 293 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 146 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS C 119 HIS D 217 HIS D 236 GLN D 399 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121465 restraints weight = 22677.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124234 restraints weight = 13288.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126044 restraints weight = 9386.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127068 restraints weight = 7537.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127874 restraints weight = 6619.149| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13120 Z= 0.156 Angle : 0.716 9.852 17864 Z= 0.336 Chirality : 0.043 0.239 1984 Planarity : 0.005 0.042 2108 Dihedral : 7.354 61.491 1808 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.33 % Allowed : 24.23 % Favored : 71.44 % 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: -0.33 (0.22), residues: 1460 helix: 0.57 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : -2.42 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 379 TYR 0.015 0.001 TYR B 182 PHE 0.020 0.001 PHE A 387 TRP 0.015 0.001 TRP C 478 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (13120) covalent geometry : angle 0.71633 / 0.34 (17864) hydrogen bonds : bond 0.03896 / 2.55 ( 780) hydrogen bonds : angle 4.81046 / 3.47 ( 2340) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8548 (tt) cc_final: 0.8316 (tt) REVERT: A 223 GLN cc_start: 0.6497 (mt0) cc_final: 0.6170 (pp30) REVERT: A 368 GLU cc_start: 0.8246 (tp30) cc_final: 0.7841 (tp30) REVERT: A 442 LEU cc_start: 0.8659 (mt) cc_final: 0.8398 (mt) REVERT: A 444 PHE cc_start: 0.8445 (m-80) cc_final: 0.7880 (m-80) REVERT: B 170 TRP cc_start: 0.8094 (t60) cc_final: 0.7824 (t60) REVERT: B 224 LEU cc_start: 0.8400 (mm) cc_final: 0.8079 (mm) REVERT: B 235 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 247 LEU cc_start: 0.8662 (mm) cc_final: 0.8083 (tt) REVERT: B 281 ILE cc_start: 0.8919 (mm) cc_final: 0.8554 (mm) REVERT: B 283 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7142 (mmt90) REVERT: B 300 ASN cc_start: 0.7523 (m-40) cc_final: 0.7021 (t0) REVERT: B 350 MET cc_start: 0.7691 (mmm) cc_final: 0.7286 (mpp) REVERT: B 380 ASP cc_start: 0.7160 (p0) cc_final: 0.6822 (p0) REVERT: B 419 ARG cc_start: 0.5607 (ptt-90) cc_final: 0.4381 (ptm160) REVERT: B 473 TRP cc_start: 0.7757 (t-100) cc_final: 0.7116 (m-90) REVERT: B 492 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: C 223 GLN cc_start: 0.6658 (mt0) cc_final: 0.6453 (pp30) REVERT: C 368 GLU cc_start: 0.8208 (tp30) cc_final: 0.7873 (tp30) REVERT: C 391 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7090 (t80) REVERT: C 444 PHE cc_start: 0.8347 (m-80) cc_final: 0.7459 (m-80) REVERT: D 170 TRP cc_start: 0.8113 (t60) cc_final: 0.6891 (t60) REVERT: D 224 LEU cc_start: 0.8284 (mm) cc_final: 0.7914 (mm) REVERT: D 237 VAL cc_start: 0.8896 (m) cc_final: 0.8666 (p) REVERT: D 247 LEU cc_start: 0.8570 (mm) cc_final: 0.8051 (tt) REVERT: D 380 ASP cc_start: 0.6702 (p0) cc_final: 0.6187 (p0) REVERT: D 473 TRP cc_start: 0.7711 (t-100) cc_final: 0.7170 (m-90) REVERT: D 476 LEU cc_start: 0.8755 (tt) cc_final: 0.7677 (mm) REVERT: D 492 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7907 (m-80) outliers start: 56 outliers final: 37 residues processed: 332 average time/residue: 0.0763 time to fit residues: 39.4019 Evaluate side-chains 319 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 HIS D 217 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.148815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121070 restraints weight = 22501.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123539 restraints weight = 13403.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125155 restraints weight = 9526.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126264 restraints weight = 7739.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126537 restraints weight = 6773.505| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13120 Z= 0.139 Angle : 0.685 10.624 17864 Z= 0.319 Chirality : 0.041 0.190 1984 Planarity : 0.005 0.045 2108 Dihedral : 6.658 59.273 1808 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.41 % Allowed : 25.77 % Favored : 69.81 % 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: 0.07 (0.22), residues: 1460 helix: 0.82 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -2.42 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 238 TYR 0.021 0.001 TYR A 407 PHE 0.011 0.001 PHE D 440 TRP 0.012 0.001 TRP C 478 HIS 0.011 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (13120) covalent geometry : angle 0.68467 / 0.32 (17864) hydrogen bonds : bond 0.03495 / 2.30 ( 780) hydrogen bonds : angle 4.61171 / 3.32 ( 2340) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8590 (tt) cc_final: 0.8346 (tt) REVERT: A 188 TRP cc_start: 0.6940 (m-10) cc_final: 0.6714 (m-10) REVERT: A 223 GLN cc_start: 0.6450 (mt0) cc_final: 0.6195 (pp30) REVERT: A 368 GLU cc_start: 0.8266 (tp30) cc_final: 0.7870 (tp30) REVERT: A 444 PHE cc_start: 0.8508 (m-80) cc_final: 0.7980 (m-80) REVERT: B 224 LEU cc_start: 0.8341 (mm) cc_final: 0.8069 (mm) REVERT: B 247 LEU cc_start: 0.8603 (mm) cc_final: 0.8039 (tt) REVERT: B 281 ILE cc_start: 0.8904 (mm) cc_final: 0.8554 (mm) REVERT: B 300 ASN cc_start: 0.7434 (m-40) cc_final: 0.6964 (t0) REVERT: B 350 MET cc_start: 0.7691 (mmm) cc_final: 0.7421 (tpp) REVERT: B 419 ARG cc_start: 0.5567 (ptt-90) cc_final: 0.4226 (ptm160) REVERT: B 473 TRP cc_start: 0.7757 (t-100) cc_final: 0.7065 (m-90) REVERT: B 492 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: C 223 GLN cc_start: 0.6669 (mt0) cc_final: 0.6455 (pp30) REVERT: C 341 LEU cc_start: 0.8479 (tp) cc_final: 0.8053 (tp) REVERT: C 368 GLU cc_start: 0.8269 (tp30) cc_final: 0.7845 (tp30) REVERT: C 444 PHE cc_start: 0.8175 (m-10) cc_final: 0.7646 (m-10) REVERT: C 459 MET cc_start: 0.5462 (ttm) cc_final: 0.4924 (ttt) REVERT: D 224 LEU cc_start: 0.8322 (mm) cc_final: 0.8062 (mm) REVERT: D 235 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7630 (tp30) REVERT: D 237 VAL cc_start: 0.8920 (m) cc_final: 0.8717 (p) REVERT: D 300 ASN cc_start: 0.6968 (t0) cc_final: 0.6698 (t0) REVERT: D 326 MET cc_start: 0.5961 (tmm) cc_final: 0.5615 (ppp) REVERT: D 380 ASP cc_start: 0.7026 (p0) cc_final: 0.6583 (p0) REVERT: D 473 TRP cc_start: 0.7827 (t-100) cc_final: 0.7160 (m-90) REVERT: D 480 MET cc_start: 0.8035 (mmt) cc_final: 0.7699 (mmm) REVERT: D 492 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: D 497 TYR cc_start: 0.7419 (m-10) cc_final: 0.7209 (m-10) outliers start: 57 outliers final: 43 residues processed: 322 average time/residue: 0.0775 time to fit residues: 39.0159 Evaluate side-chains 317 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 ASN B 119 HIS B 217 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 HIS ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN D 434 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116786 restraints weight = 22573.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119397 restraints weight = 13158.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121109 restraints weight = 9320.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122008 restraints weight = 7541.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122709 restraints weight = 6686.127| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13120 Z= 0.183 Angle : 0.727 11.313 17864 Z= 0.342 Chirality : 0.043 0.182 1984 Planarity : 0.005 0.044 2108 Dihedral : 6.695 56.869 1808 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.65 % Allowed : 24.85 % Favored : 69.50 % 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: -0.01 (0.22), residues: 1460 helix: 0.85 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -2.57 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 238 TYR 0.017 0.002 TYR A 407 PHE 0.014 0.001 PHE C 120 TRP 0.013 0.001 TRP C 394 HIS 0.007 0.001 HIS C 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (13120) covalent geometry : angle 0.72698 / 0.34 (17864) hydrogen bonds : bond 0.03745 / 2.47 ( 780) hydrogen bonds : angle 4.67145 / 3.37 ( 2340) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8616 (tt) cc_final: 0.8413 (tt) REVERT: A 223 GLN cc_start: 0.6594 (mt0) cc_final: 0.6322 (pp30) REVERT: A 368 GLU cc_start: 0.8301 (tp30) cc_final: 0.8031 (tp30) REVERT: A 444 PHE cc_start: 0.8593 (m-80) cc_final: 0.8073 (m-80) REVERT: B 224 LEU cc_start: 0.8352 (mm) cc_final: 0.8072 (mm) REVERT: B 235 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7432 (tp30) REVERT: B 281 ILE cc_start: 0.8960 (mm) cc_final: 0.8557 (mm) REVERT: B 300 ASN cc_start: 0.7647 (m-40) cc_final: 0.7086 (t0) REVERT: B 376 MET cc_start: 0.7073 (tpt) cc_final: 0.6836 (tmm) REVERT: B 419 ARG cc_start: 0.5791 (ptt-90) cc_final: 0.4245 (ptm160) REVERT: B 453 PHE cc_start: 0.7778 (t80) cc_final: 0.7514 (t80) REVERT: B 473 TRP cc_start: 0.7744 (t-100) cc_final: 0.7081 (m-90) REVERT: B 492 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: C 223 GLN cc_start: 0.6770 (mt0) cc_final: 0.6514 (pp30) REVERT: C 341 LEU cc_start: 0.8628 (tp) cc_final: 0.8286 (tp) REVERT: C 368 GLU cc_start: 0.8321 (tp30) cc_final: 0.7993 (tp30) REVERT: C 444 PHE cc_start: 0.8136 (m-10) cc_final: 0.7833 (m-10) REVERT: D 224 LEU cc_start: 0.8355 (mm) cc_final: 0.8071 (mm) REVERT: D 237 VAL cc_start: 0.9035 (m) cc_final: 0.8761 (p) REVERT: D 300 ASN cc_start: 0.7402 (t0) cc_final: 0.6893 (t0) REVERT: D 326 MET cc_start: 0.6085 (tmm) cc_final: 0.5599 (ppp) REVERT: D 449 MET cc_start: 0.5862 (tmm) cc_final: 0.4993 (tpt) REVERT: D 473 TRP cc_start: 0.7815 (t-100) cc_final: 0.7112 (m-90) REVERT: D 492 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: D 497 TYR cc_start: 0.7666 (m-10) cc_final: 0.7441 (m-10) outliers start: 73 outliers final: 58 residues processed: 316 average time/residue: 0.0844 time to fit residues: 41.7564 Evaluate side-chains 317 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 HIS ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119885 restraints weight = 22370.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122538 restraints weight = 13084.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124264 restraints weight = 9184.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125172 restraints weight = 7384.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125350 restraints weight = 6532.886| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13120 Z= 0.134 Angle : 0.690 11.040 17864 Z= 0.319 Chirality : 0.040 0.215 1984 Planarity : 0.004 0.044 2108 Dihedral : 6.354 58.684 1808 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.34 % Allowed : 27.09 % Favored : 67.57 % 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: 0.17 (0.22), residues: 1460 helix: 0.99 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -2.52 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 238 TYR 0.016 0.001 TYR D 182 PHE 0.011 0.001 PHE C 120 TRP 0.010 0.001 TRP C 496 HIS 0.004 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13120) covalent geometry : angle 0.68992 / 0.32 (17864) hydrogen bonds : bond 0.03396 / 2.24 ( 780) hydrogen bonds : angle 4.51910 / 3.26 ( 2340) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8621 (tt) cc_final: 0.8419 (tt) REVERT: A 223 GLN cc_start: 0.6572 (mt0) cc_final: 0.6326 (pp30) REVERT: A 368 GLU cc_start: 0.8260 (tp30) cc_final: 0.7883 (tp30) REVERT: A 383 ASN cc_start: 0.8677 (m110) cc_final: 0.8472 (m-40) REVERT: A 436 TYR cc_start: 0.8534 (t80) cc_final: 0.8333 (t80) REVERT: A 444 PHE cc_start: 0.8615 (m-80) cc_final: 0.8089 (m-80) REVERT: B 224 LEU cc_start: 0.8269 (mm) cc_final: 0.7991 (mm) REVERT: B 281 ILE cc_start: 0.8948 (mm) cc_final: 0.8564 (mt) REVERT: B 300 ASN cc_start: 0.7470 (m-40) cc_final: 0.6965 (t0) REVERT: B 376 MET cc_start: 0.6930 (tpt) cc_final: 0.6630 (tmm) REVERT: B 408 GLN cc_start: 0.7902 (mt0) cc_final: 0.7574 (mm110) REVERT: B 419 ARG cc_start: 0.5676 (ptt-90) cc_final: 0.4094 (ptm160) REVERT: B 428 LEU cc_start: 0.9148 (tp) cc_final: 0.8785 (pp) REVERT: B 453 PHE cc_start: 0.7690 (t80) cc_final: 0.7456 (t80) REVERT: B 473 TRP cc_start: 0.7722 (t-100) cc_final: 0.7074 (m-90) REVERT: C 223 GLN cc_start: 0.6741 (mt0) cc_final: 0.6496 (pp30) REVERT: C 340 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8598 (tp) REVERT: C 341 LEU cc_start: 0.8626 (tp) cc_final: 0.8199 (tp) REVERT: C 368 GLU cc_start: 0.8289 (tp30) cc_final: 0.7926 (tp30) REVERT: D 173 MET cc_start: 0.9033 (ppp) cc_final: 0.8742 (ppp) REVERT: D 224 LEU cc_start: 0.8287 (mm) cc_final: 0.7961 (mm) REVERT: D 237 VAL cc_start: 0.8979 (m) cc_final: 0.8735 (p) REVERT: D 300 ASN cc_start: 0.7091 (t0) cc_final: 0.6740 (t0) REVERT: D 326 MET cc_start: 0.6138 (tmm) cc_final: 0.5672 (ppp) REVERT: D 419 ARG cc_start: 0.4976 (ptt-90) cc_final: 0.4190 (ptm160) REVERT: D 449 MET cc_start: 0.5742 (tmm) cc_final: 0.5052 (tpt) REVERT: D 473 TRP cc_start: 0.7821 (t-100) cc_final: 0.7163 (m-90) REVERT: D 492 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7975 (m-80) outliers start: 69 outliers final: 51 residues processed: 325 average time/residue: 0.0793 time to fit residues: 40.0575 Evaluate side-chains 318 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 492 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 110 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS D 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.148373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120122 restraints weight = 22336.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122808 restraints weight = 12826.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124564 restraints weight = 8992.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125440 restraints weight = 7215.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126193 restraints weight = 6393.833| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13120 Z= 0.131 Angle : 0.688 10.901 17864 Z= 0.319 Chirality : 0.040 0.154 1984 Planarity : 0.004 0.043 2108 Dihedral : 6.183 59.896 1808 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.42 % Allowed : 27.09 % Favored : 67.49 % 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: 0.34 (0.22), residues: 1460 helix: 1.11 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -2.46 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.016 0.001 TYR D 182 PHE 0.017 0.001 PHE C 444 TRP 0.017 0.001 TRP A 478 HIS 0.004 0.001 HIS C 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13120) covalent geometry : angle 0.68839 / 0.32 (17864) hydrogen bonds : bond 0.03365 / 2.23 ( 780) hydrogen bonds : angle 4.42886 / 3.20 ( 2340) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8646 (tt) cc_final: 0.8443 (tt) REVERT: A 368 GLU cc_start: 0.8214 (tp30) cc_final: 0.7854 (tp30) REVERT: A 444 PHE cc_start: 0.8572 (m-80) cc_final: 0.7719 (m-80) REVERT: B 115 MET cc_start: 0.7934 (tpt) cc_final: 0.7648 (tpt) REVERT: B 173 MET cc_start: 0.8998 (ppp) cc_final: 0.8749 (ppp) REVERT: B 224 LEU cc_start: 0.8212 (mm) cc_final: 0.7946 (mm) REVERT: B 281 ILE cc_start: 0.8970 (mm) cc_final: 0.8388 (tt) REVERT: B 300 ASN cc_start: 0.7435 (m-40) cc_final: 0.6957 (t0) REVERT: B 391 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.6171 (m-80) REVERT: B 419 ARG cc_start: 0.5633 (ptt-90) cc_final: 0.4056 (ptm160) REVERT: B 428 LEU cc_start: 0.9200 (tp) cc_final: 0.8773 (pp) REVERT: B 453 PHE cc_start: 0.7567 (t80) cc_final: 0.7352 (t80) REVERT: B 473 TRP cc_start: 0.7647 (t-100) cc_final: 0.7018 (m-90) REVERT: B 492 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: C 340 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8581 (tp) REVERT: C 341 LEU cc_start: 0.8617 (tp) cc_final: 0.8176 (tp) REVERT: C 352 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8588 (tt) REVERT: C 368 GLU cc_start: 0.8296 (tp30) cc_final: 0.7872 (tp30) REVERT: D 173 MET cc_start: 0.9005 (ppp) cc_final: 0.8770 (ppp) REVERT: D 224 LEU cc_start: 0.8282 (mm) cc_final: 0.8042 (mm) REVERT: D 237 VAL cc_start: 0.8975 (m) cc_final: 0.8758 (p) REVERT: D 300 ASN cc_start: 0.7170 (t0) cc_final: 0.6762 (t0) REVERT: D 326 MET cc_start: 0.6192 (tmm) cc_final: 0.5800 (ppp) REVERT: D 419 ARG cc_start: 0.4959 (ptt-90) cc_final: 0.4093 (ptm160) REVERT: D 449 MET cc_start: 0.5658 (tmm) cc_final: 0.5132 (tpt) REVERT: D 473 TRP cc_start: 0.7705 (t-100) cc_final: 0.7137 (m-90) outliers start: 70 outliers final: 52 residues processed: 324 average time/residue: 0.0846 time to fit residues: 42.3838 Evaluate side-chains 318 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 488 GLN Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN B 217 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 HIS B 488 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 217 HIS D 223 GLN ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133402 restraints weight = 22185.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135944 restraints weight = 12969.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137619 restraints weight = 9107.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138572 restraints weight = 7298.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139252 restraints weight = 6417.450| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13120 Z= 0.136 Angle : 0.709 11.009 17864 Z= 0.329 Chirality : 0.040 0.143 1984 Planarity : 0.004 0.043 2108 Dihedral : 6.118 59.971 1808 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.03 % Allowed : 28.10 % Favored : 66.87 % 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: 0.37 (0.22), residues: 1460 helix: 1.13 (0.16), residues: 1092 sheet: None (None), residues: 0 loop : -2.47 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.017 0.001 TYR D 182 PHE 0.010 0.001 PHE C 462 TRP 0.017 0.001 TRP A 478 HIS 0.005 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13120) covalent geometry : angle 0.70918 / 0.33 (17864) hydrogen bonds : bond 0.03387 / 2.23 ( 780) hydrogen bonds : angle 4.41374 / 3.20 ( 2340) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8391 (tp30) cc_final: 0.8050 (tp30) REVERT: A 444 PHE cc_start: 0.8669 (m-80) cc_final: 0.8165 (m-80) REVERT: B 173 MET cc_start: 0.8884 (ppp) cc_final: 0.8680 (ppp) REVERT: B 224 LEU cc_start: 0.8111 (mm) cc_final: 0.7825 (mm) REVERT: B 281 ILE cc_start: 0.8854 (mm) cc_final: 0.8317 (tt) REVERT: B 300 ASN cc_start: 0.7406 (m-40) cc_final: 0.7005 (t0) REVERT: B 391 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.6018 (m-80) REVERT: B 419 ARG cc_start: 0.5626 (ptt-90) cc_final: 0.4030 (ptm160) REVERT: B 428 LEU cc_start: 0.9159 (tp) cc_final: 0.8803 (pp) REVERT: B 492 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: C 340 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8605 (tp) REVERT: C 341 LEU cc_start: 0.8602 (tp) cc_final: 0.8199 (tp) REVERT: C 352 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8622 (tt) REVERT: C 368 GLU cc_start: 0.8335 (tp30) cc_final: 0.7999 (tp30) REVERT: C 444 PHE cc_start: 0.8230 (m-10) cc_final: 0.7709 (m-10) REVERT: D 224 LEU cc_start: 0.8210 (mm) cc_final: 0.7987 (mm) REVERT: D 237 VAL cc_start: 0.8898 (m) cc_final: 0.8670 (p) REVERT: D 300 ASN cc_start: 0.7151 (t0) cc_final: 0.6767 (t0) REVERT: D 449 MET cc_start: 0.5651 (tmm) cc_final: 0.5167 (tpt) REVERT: D 473 TRP cc_start: 0.7606 (t-100) cc_final: 0.7105 (m-90) outliers start: 65 outliers final: 52 residues processed: 314 average time/residue: 0.0796 time to fit residues: 39.1491 Evaluate side-chains 317 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 488 GLN Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.0270 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 0.0970 chunk 139 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 HIS B 434 HIS B 488 GLN C 236 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.163221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137695 restraints weight = 22359.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140454 restraints weight = 12688.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142258 restraints weight = 8690.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143129 restraints weight = 6849.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143840 restraints weight = 6005.945| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13120 Z= 0.123 Angle : 0.713 11.825 17864 Z= 0.331 Chirality : 0.039 0.198 1984 Planarity : 0.004 0.041 2108 Dihedral : 5.786 53.668 1808 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.02 % Allowed : 29.57 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.22), residues: 1460 helix: 1.18 (0.16), residues: 1096 sheet: None (None), residues: 0 loop : -2.62 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.021 0.001 TYR B 405 PHE 0.023 0.001 PHE D 440 TRP 0.017 0.001 TRP A 478 HIS 0.006 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13120) covalent geometry : angle 0.71280 / 0.33 (17864) hydrogen bonds : bond 0.03267 / 2.17 ( 780) hydrogen bonds : angle 4.33952 / 3.13 ( 2340) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLU cc_start: 0.8392 (tp30) cc_final: 0.7942 (tp30) REVERT: A 374 ASP cc_start: 0.8239 (t70) cc_final: 0.7776 (t0) REVERT: A 444 PHE cc_start: 0.8609 (m-80) cc_final: 0.8261 (m-80) REVERT: B 300 ASN cc_start: 0.7233 (m-40) cc_final: 0.6864 (t0) REVERT: B 391 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: B 408 GLN cc_start: 0.7753 (mt0) cc_final: 0.7506 (mm-40) REVERT: B 428 LEU cc_start: 0.9140 (tp) cc_final: 0.8940 (pp) REVERT: C 341 LEU cc_start: 0.8581 (tp) cc_final: 0.8153 (tp) REVERT: C 368 GLU cc_start: 0.8302 (tp30) cc_final: 0.7976 (tp30) REVERT: C 449 MET cc_start: 0.7330 (tpp) cc_final: 0.7085 (tpt) REVERT: D 224 LEU cc_start: 0.8220 (mm) cc_final: 0.7991 (mm) REVERT: D 235 GLU cc_start: 0.7374 (tp30) cc_final: 0.6864 (tp30) REVERT: D 239 PHE cc_start: 0.8455 (m-10) cc_final: 0.8246 (m-80) REVERT: D 300 ASN cc_start: 0.7001 (t0) cc_final: 0.6639 (t0) REVERT: D 391 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: D 449 MET cc_start: 0.5613 (tmm) cc_final: 0.5145 (tpt) REVERT: D 473 TRP cc_start: 0.7641 (t-100) cc_final: 0.7130 (m-90) outliers start: 52 outliers final: 38 residues processed: 307 average time/residue: 0.0811 time to fit residues: 40.1729 Evaluate side-chains 306 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 488 GLN Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 217 HIS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 90 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN B 217 HIS B 434 HIS ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS D 223 GLN D 434 HIS ** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.163225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.137510 restraints weight = 22111.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140190 restraints weight = 12545.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141919 restraints weight = 8673.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142840 restraints weight = 6865.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143610 restraints weight = 6023.567| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13120 Z= 0.131 Angle : 0.748 12.050 17864 Z= 0.347 Chirality : 0.040 0.208 1984 Planarity : 0.004 0.041 2108 Dihedral : 5.727 51.522 1808 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.33 % Allowed : 30.80 % Favored : 65.87 % 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: 0.38 (0.22), residues: 1460 helix: 1.09 (0.16), residues: 1112 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.030 0.001 TYR B 405 PHE 0.022 0.001 PHE D 440 TRP 0.020 0.001 TRP A 478 HIS 0.005 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13120) covalent geometry : angle 0.74817 / 0.35 (17864) hydrogen bonds : bond 0.03351 / 2.21 ( 780) hydrogen bonds : angle 4.32737 / 3.14 ( 2340) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.8041 (m-80) cc_final: 0.7673 (t80) REVERT: A 368 GLU cc_start: 0.8376 (tp30) cc_final: 0.7948 (tp30) REVERT: A 374 ASP cc_start: 0.8158 (t70) cc_final: 0.7753 (t0) REVERT: A 444 PHE cc_start: 0.8572 (m-80) cc_final: 0.7959 (m-80) REVERT: B 300 ASN cc_start: 0.7264 (m-40) cc_final: 0.6866 (t0) REVERT: C 368 GLU cc_start: 0.8302 (tp30) cc_final: 0.7994 (tp30) REVERT: C 449 MET cc_start: 0.7296 (tpp) cc_final: 0.7058 (tpt) REVERT: D 203 LEU cc_start: 0.8435 (mt) cc_final: 0.7698 (tp) REVERT: D 300 ASN cc_start: 0.7030 (t0) cc_final: 0.6663 (t0) REVERT: D 391 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: D 449 MET cc_start: 0.5708 (tmm) cc_final: 0.5227 (tpt) REVERT: D 473 TRP cc_start: 0.7626 (t-100) cc_final: 0.7159 (m-90) REVERT: D 476 LEU cc_start: 0.8592 (tt) cc_final: 0.8384 (tt) outliers start: 43 outliers final: 33 residues processed: 290 average time/residue: 0.0837 time to fit residues: 38.9496 Evaluate side-chains 287 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain B residue 134 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain C residue 134 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 349 PHE Chi-restraints excluded: chain C residue 438 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 134 PHE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 217 HIS Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN B 217 HIS B 434 HIS ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS D 223 GLN D 434 HIS ** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.160948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134894 restraints weight = 22231.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.137529 restraints weight = 12776.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139073 restraints weight = 8886.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140300 restraints weight = 7113.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140618 restraints weight = 6173.846| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13120 Z= 0.158 Angle : 0.765 11.571 17864 Z= 0.359 Chirality : 0.041 0.189 1984 Planarity : 0.005 0.042 2108 Dihedral : 5.797 51.026 1808 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.48 % Allowed : 31.04 % Favored : 65.48 % 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: 0.28 (0.22), residues: 1460 helix: 1.01 (0.16), residues: 1112 sheet: None (None), residues: 0 loop : -2.53 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.033 0.002 TYR D 405 PHE 0.021 0.001 PHE D 440 TRP 0.019 0.001 TRP C 478 HIS 0.019 0.002 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (13120) covalent geometry : angle 0.76514 / 0.36 (17864) hydrogen bonds : bond 0.03530 / 2.34 ( 780) hydrogen bonds : angle 4.35902 / 3.17 ( 2340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.60 seconds wall clock time: 35 minutes 50.38 seconds (2150.38 seconds total)