Starting phenix.real_space_refine on Thu Jul 2 16:26:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d67_46588/07_2026/9d67_46588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d67_46588/07_2026/9d67_46588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d67_46588/07_2026/9d67_46588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d67_46588/07_2026/9d67_46588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d67_46588/07_2026/9d67_46588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d67_46588/07_2026/9d67_46588.map" } resolution = 2.87 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= 0.003 sd= 0.151 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: 6 Type Number sf(0) Gaussians Hg 3 10.96 5 S 60 5.16 5 Na 9 4.78 5 C 6087 2.51 5 N 1479 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 9297 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "B" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "C" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 9 Ad-hoc single atom residues: {' NA': 3, ' HG': 1} Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain breaks: 4 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 9 Ad-hoc single atom residues: {' HG': 1, ' NA': 3} Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain breaks: 4 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 9 Ad-hoc single atom residues: {' NA': 3, ' HG': 1} Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 49.179 82.768 22.871 1.00 85.37 S ATOM 2858 SG CYS A 441 48.431 81.437 25.785 1.00 81.69 S ATOM 4662 SG CYS B 269 78.219 37.296 22.873 1.00 85.37 S ATOM 5943 SG CYS B 441 77.441 38.609 25.787 1.00 81.69 S ATOM 7747 SG CYS C 269 24.317 34.880 22.863 1.00 85.37 S ATOM 9028 SG CYS C 441 25.843 34.898 25.778 1.00 81.69 S Time building chain proxies: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9297 At special positions: 0 Unit cell: (105.448, 103.296, 69.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 3 79.96 S 60 16.00 Na 9 11.00 O 1659 8.00 N 1479 7.00 C 6087 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: 0.80 Conformation dependent library (CDL) restraints added in 365.9 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAS A 600 " pdb=" CB DAS B 605 " pdb=" CB DAS C 600 " Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 85.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.650A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 82 removed outlier: 4.480A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.822A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.651A pdb=" N GLY A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.678A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.590A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.599A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.869A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.109A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.581A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 418' Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.858A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.563A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.741A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.651A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 removed outlier: 4.480A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.822A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 117 removed outlier: 3.650A pdb=" N GLY B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.679A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 211 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 273 removed outlier: 3.589A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.599A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.869A pdb=" N ARG B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.108A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.581A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 418' Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.859A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.563A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.741A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.650A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 82 removed outlier: 4.480A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.821A pdb=" N LEU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 117 removed outlier: 3.651A pdb=" N GLY C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.678A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.590A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.599A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.869A pdb=" N ARG C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.108A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.581A pdb=" N VAL C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.859A pdb=" N VAL C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.563A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.741A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 726 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1788 1.33 - 1.45: 1951 1.45 - 1.57: 5567 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 9417 Sorted by residual: bond pdb=" N VAL C 417 " pdb=" CA VAL C 417 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.80e+00 bond pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.34e+00 bond pdb=" N VAL B 417 " pdb=" CA VAL B 417 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.28e+00 bond pdb=" N LEU C 328 " pdb=" CA LEU C 328 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.35e-02 5.49e+03 5.57e+00 bond pdb=" N ARG A 445 " pdb=" CA ARG A 445 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.45e+00 ... (remaining 9412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 12180 1.26 - 2.52: 459 2.52 - 3.78: 112 3.78 - 5.04: 29 5.04 - 6.29: 3 Bond angle restraints: 12783 Sorted by residual: angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.23 117.53 3.70 1.07e+00 8.73e-01 1.19e+01 angle pdb=" CA PRO C 412 " pdb=" C PRO C 412 " pdb=" O PRO C 412 " ideal model delta sigma weight residual 121.23 117.53 3.70 1.07e+00 8.73e-01 1.19e+01 angle pdb=" CA PRO B 412 " pdb=" C PRO B 412 " pdb=" O PRO B 412 " ideal model delta sigma weight residual 121.23 117.56 3.67 1.07e+00 8.73e-01 1.18e+01 angle pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" O VAL A 417 " ideal model delta sigma weight residual 120.85 117.88 2.97 1.06e+00 8.90e-01 7.87e+00 angle pdb=" CA VAL C 417 " pdb=" C VAL C 417 " pdb=" O VAL C 417 " ideal model delta sigma weight residual 120.85 117.88 2.97 1.06e+00 8.90e-01 7.86e+00 ... (remaining 12778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 5238 25.63 - 51.26: 330 51.26 - 76.90: 42 76.90 - 102.53: 3 102.53 - 128.16: 3 Dihedral angle restraints: 5616 sinusoidal: 2127 harmonic: 3489 Sorted by residual: dihedral pdb=" CA DAS B 605 " pdb=" CB DAS B 605 " pdb=" CG DAS B 605 " pdb=" OD1 DAS B 605 " ideal model delta sinusoidal sigma weight residual -30.00 -158.16 128.16 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" CA DAS A 600 " pdb=" CB DAS A 600 " pdb=" CG DAS A 600 " pdb=" OD1 DAS A 600 " ideal model delta sinusoidal sigma weight residual -30.00 -158.16 128.16 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" CA DAS C 600 " pdb=" CB DAS C 600 " pdb=" CG DAS C 600 " pdb=" OD1 DAS C 600 " ideal model delta sinusoidal sigma weight residual -30.00 -158.14 128.14 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 5613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1191 0.040 - 0.080: 354 0.080 - 0.120: 69 0.120 - 0.160: 9 0.160 - 0.200: 3 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CA MET B 367 " pdb=" N MET B 367 " pdb=" C MET B 367 " pdb=" CB MET B 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA MET C 367 " pdb=" N MET C 367 " pdb=" C MET C 367 " pdb=" CB MET C 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1623 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 166 " -0.250 9.50e-02 1.11e+02 1.13e-01 9.43e+00 pdb=" NE ARG A 166 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 166 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 166 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 166 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 166 " 0.250 9.50e-02 1.11e+02 1.13e-01 9.42e+00 pdb=" NE ARG C 166 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG C 166 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG C 166 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 166 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 166 " 0.250 9.50e-02 1.11e+02 1.13e-01 9.35e+00 pdb=" NE ARG B 166 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 166 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 166 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 166 " 0.002 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 221 2.69 - 3.25: 10163 3.25 - 3.80: 15569 3.80 - 4.35: 20822 4.35 - 4.90: 34232 Nonbonded interactions: 81007 Sorted by model distance: nonbonded pdb=" O THR A 364 " pdb="NA NA A 602 " model vdw 2.143 3.210 nonbonded pdb=" O THR B 364 " pdb="NA NA B 603 " model vdw 2.143 3.210 nonbonded pdb=" O THR C 364 " pdb="NA NA C 602 " model vdw 2.143 3.210 nonbonded pdb=" O ALA A 408 " pdb="NA NA A 602 " model vdw 2.161 3.210 nonbonded pdb=" O ALA B 408 " pdb="NA NA B 603 " model vdw 2.161 3.210 ... (remaining 81002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 470 or resid 601 through 603)) selection = (chain 'B' and (resid 17 through 470 or resid 602 through 604)) selection = (chain 'C' and (resid 17 through 470 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 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 : 0.003 0.038 9417 Z= 0.173 Angle : 0.605 6.295 12783 Z= 0.326 Chirality : 0.040 0.200 1626 Planarity : 0.007 0.113 1557 Dihedral : 16.101 128.161 3366 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 22.55 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1200 helix: 1.15 (0.17), residues: 924 sheet: -0.46 (0.66), residues: 54 loop : -1.11 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 166 TYR 0.014 0.001 TYR B 97 PHE 0.016 0.002 PHE C 240 TRP 0.004 0.001 TRP A 256 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 ( 9417) covalent geometry : angle 0.60451 / 0.33 (12783) hydrogen bonds : bond 0.13956 / 9.56 ( 726) hydrogen bonds : angle 6.27246 / 4.44 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7113 (t80) cc_final: 0.6593 (t80) REVERT: A 103 LEU cc_start: 0.7427 (mm) cc_final: 0.7209 (mm) REVERT: A 117 LYS cc_start: 0.7594 (mtmm) cc_final: 0.6834 (mttp) REVERT: A 142 MET cc_start: 0.8083 (tpp) cc_final: 0.7764 (mmp) REVERT: A 205 MET cc_start: 0.7813 (ptt) cc_final: 0.7247 (pmm) REVERT: A 207 SER cc_start: 0.7809 (p) cc_final: 0.7498 (m) REVERT: A 255 MET cc_start: 0.8217 (tpp) cc_final: 0.7881 (mmm) REVERT: A 258 MET cc_start: 0.7963 (tpp) cc_final: 0.7721 (ttt) REVERT: A 315 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.6987 (ttm110) REVERT: A 352 LYS cc_start: 0.6843 (mttp) cc_final: 0.6613 (mtmm) REVERT: B 205 MET cc_start: 0.8009 (ptt) cc_final: 0.7295 (pmm) REVERT: B 255 MET cc_start: 0.8249 (tpp) cc_final: 0.7857 (mmm) REVERT: B 258 MET cc_start: 0.8131 (tpp) cc_final: 0.7918 (ttt) REVERT: B 277 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6502 (mp0) REVERT: B 315 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6999 (ttm170) REVERT: B 352 LYS cc_start: 0.6964 (mttp) cc_final: 0.6729 (mtmm) REVERT: B 356 ARG cc_start: 0.6903 (mmt180) cc_final: 0.6559 (mmt180) REVERT: B 399 ILE cc_start: 0.8138 (mm) cc_final: 0.7898 (mt) REVERT: C 60 MET cc_start: 0.8451 (mmm) cc_final: 0.8251 (mmm) REVERT: C 99 PHE cc_start: 0.7593 (t80) cc_final: 0.7392 (t80) REVERT: C 138 THR cc_start: 0.6518 (t) cc_final: 0.6176 (m) REVERT: C 205 MET cc_start: 0.7997 (ptt) cc_final: 0.7545 (ptm) REVERT: C 241 ASN cc_start: 0.8351 (t0) cc_final: 0.8062 (m-40) REVERT: C 315 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7067 (ttm110) REVERT: C 318 MET cc_start: 0.6261 (tpt) cc_final: 0.6035 (tpp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.5081 time to fit residues: 121.1153 Evaluate side-chains 169 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN A 347 ASN B 322 GLN B 347 ASN C 322 GLN C 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.184534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149681 restraints weight = 2672.838| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 0.63 r_work: 0.3508 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9417 Z= 0.154 Angle : 0.551 5.476 12783 Z= 0.288 Chirality : 0.040 0.150 1626 Planarity : 0.004 0.027 1557 Dihedral : 6.733 104.559 1287 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.87 % Allowed : 21.66 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.23), residues: 1200 helix: 1.41 (0.16), residues: 915 sheet: 0.23 (0.60), residues: 48 loop : -0.80 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 166 TYR 0.008 0.001 TYR B 97 PHE 0.014 0.002 PHE B 240 TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 9417) covalent geometry : angle 0.55062 / 0.29 (12783) hydrogen bonds : bond 0.04561 / 3.15 ( 726) hydrogen bonds : angle 4.72190 / 3.40 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.360 Fit side-chains REVERT: A 99 PHE cc_start: 0.7673 (t80) cc_final: 0.7404 (t80) REVERT: A 117 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7682 (mttp) REVERT: A 315 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7342 (ttm110) REVERT: A 353 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7740 (mtm-85) REVERT: A 442 LEU cc_start: 0.7609 (tp) cc_final: 0.7360 (tt) REVERT: A 444 ASP cc_start: 0.7997 (t0) cc_final: 0.7697 (t70) REVERT: B 68 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7362 (tp) REVERT: B 205 MET cc_start: 0.8195 (ptt) cc_final: 0.7994 (ptm) REVERT: B 277 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6542 (mp0) REVERT: B 304 ILE cc_start: 0.7876 (tt) cc_final: 0.7573 (mt) REVERT: B 315 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7388 (ttm170) REVERT: C 68 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7388 (tp) REVERT: C 138 THR cc_start: 0.7029 (t) cc_final: 0.6633 (m) REVERT: C 163 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.7999 (ptpt) REVERT: C 205 MET cc_start: 0.8230 (ptt) cc_final: 0.7963 (ptm) REVERT: C 228 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7696 (mmtm) REVERT: C 315 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7423 (ttm110) REVERT: C 444 ASP cc_start: 0.8190 (t0) cc_final: 0.7877 (t70) outliers start: 29 outliers final: 4 residues processed: 198 average time/residue: 0.5177 time to fit residues: 109.8879 Evaluate side-chains 166 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 229 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.195259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.164073 restraints weight = 2396.817| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 0.52 r_work: 0.3546 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9417 Z= 0.125 Angle : 0.496 5.204 12783 Z= 0.259 Chirality : 0.039 0.162 1626 Planarity : 0.003 0.029 1557 Dihedral : 6.342 90.354 1287 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.76 % Allowed : 22.26 % Favored : 73.99 % 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: 1.52 (0.23), residues: 1200 helix: 1.59 (0.16), residues: 918 sheet: 0.10 (0.60), residues: 48 loop : -1.00 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.009 0.001 TYR A 162 PHE 0.011 0.001 PHE C 240 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9417) covalent geometry : angle 0.49566 / 0.26 (12783) hydrogen bonds : bond 0.03996 / 2.75 ( 726) hydrogen bonds : angle 4.47064 / 3.23 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.406 Fit side-chains REVERT: A 99 PHE cc_start: 0.7497 (t80) cc_final: 0.7191 (t80) REVERT: A 117 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7625 (mttp) REVERT: A 138 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6738 (m) REVERT: A 277 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6006 (pm20) REVERT: A 303 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7685 (tp) REVERT: A 315 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7326 (ttm110) REVERT: A 320 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7947 (mtp) REVERT: A 353 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7732 (mtm-85) REVERT: A 356 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6806 (mmt180) REVERT: A 444 ASP cc_start: 0.7988 (t0) cc_final: 0.7687 (t0) REVERT: B 48 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7632 (mp0) REVERT: B 68 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7410 (tp) REVERT: B 138 THR cc_start: 0.7046 (OUTLIER) cc_final: 0.6734 (m) REVERT: B 167 GLU cc_start: 0.7775 (pp20) cc_final: 0.7471 (pp20) REVERT: B 205 MET cc_start: 0.8195 (ptt) cc_final: 0.7992 (ptm) REVERT: B 228 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7670 (mmtm) REVERT: B 258 MET cc_start: 0.8432 (tpp) cc_final: 0.8081 (tpt) REVERT: B 272 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6939 (mp0) REVERT: B 277 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6496 (mp0) REVERT: B 304 ILE cc_start: 0.7820 (tt) cc_final: 0.7613 (mt) REVERT: B 315 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7398 (ttm170) REVERT: B 445 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6990 (mtt90) REVERT: C 68 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7355 (tp) REVERT: C 138 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6725 (m) REVERT: C 205 MET cc_start: 0.8136 (ptt) cc_final: 0.7868 (ptm) REVERT: C 228 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7630 (mmtm) REVERT: C 277 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6348 (pm20) REVERT: C 304 ILE cc_start: 0.7988 (tt) cc_final: 0.7680 (mt) REVERT: C 315 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7480 (ttm110) REVERT: C 419 MET cc_start: 0.8748 (mmm) cc_final: 0.8514 (tpp) REVERT: C 442 LEU cc_start: 0.7573 (tp) cc_final: 0.7297 (tt) REVERT: C 444 ASP cc_start: 0.8115 (t0) cc_final: 0.7782 (t70) outliers start: 38 outliers final: 9 residues processed: 214 average time/residue: 0.5132 time to fit residues: 117.6087 Evaluate side-chains 176 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.199008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164893 restraints weight = 2306.252| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 0.64 r_work: 0.3657 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9417 Z= 0.128 Angle : 0.501 6.112 12783 Z= 0.260 Chirality : 0.039 0.135 1626 Planarity : 0.003 0.031 1557 Dihedral : 5.797 77.912 1287 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.36 % Allowed : 23.44 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.23), residues: 1200 helix: 1.61 (0.16), residues: 918 sheet: 0.08 (0.63), residues: 48 loop : -1.01 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.011 0.001 TYR A 162 PHE 0.013 0.001 PHE B 240 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9417) covalent geometry : angle 0.50113 / 0.26 (12783) hydrogen bonds : bond 0.03947 / 2.72 ( 726) hydrogen bonds : angle 4.42293 / 3.21 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.343 Fit side-chains REVERT: A 99 PHE cc_start: 0.7572 (t80) cc_final: 0.7101 (t80) REVERT: A 101 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7593 (p) REVERT: A 117 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7605 (mttp) REVERT: A 138 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6561 (m) REVERT: A 277 GLU cc_start: 0.6342 (tm-30) cc_final: 0.6107 (mp0) REVERT: A 303 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7613 (tp) REVERT: A 315 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7233 (ttm110) REVERT: A 353 ARG cc_start: 0.7908 (mtm180) cc_final: 0.7680 (mtm-85) REVERT: A 356 ARG cc_start: 0.6988 (mmt180) cc_final: 0.6696 (mmt180) REVERT: A 444 ASP cc_start: 0.7987 (t0) cc_final: 0.7723 (t0) REVERT: B 68 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7336 (tp) REVERT: B 138 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6621 (m) REVERT: B 205 MET cc_start: 0.8149 (ptt) cc_final: 0.7946 (ptm) REVERT: B 228 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7524 (mmtm) REVERT: B 258 MET cc_start: 0.8415 (tpp) cc_final: 0.8132 (tpt) REVERT: B 277 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6447 (pm20) REVERT: B 315 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7306 (ttm170) REVERT: C 68 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7217 (tp) REVERT: C 86 VAL cc_start: 0.6028 (OUTLIER) cc_final: 0.5824 (p) REVERT: C 138 THR cc_start: 0.7020 (OUTLIER) cc_final: 0.6618 (m) REVERT: C 163 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.7870 (ptpt) REVERT: C 205 MET cc_start: 0.8074 (ptt) cc_final: 0.7758 (ptm) REVERT: C 228 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7408 (mtmt) REVERT: C 235 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7944 (tt) REVERT: C 277 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6297 (pm20) REVERT: C 304 ILE cc_start: 0.7776 (tt) cc_final: 0.7461 (mt) REVERT: C 315 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7415 (ttm110) REVERT: C 419 MET cc_start: 0.8873 (mmm) cc_final: 0.8487 (tpp) REVERT: C 442 LEU cc_start: 0.7474 (tp) cc_final: 0.7202 (tt) REVERT: C 444 ASP cc_start: 0.8011 (t0) cc_final: 0.7760 (t70) outliers start: 34 outliers final: 12 residues processed: 193 average time/residue: 0.4737 time to fit residues: 98.4702 Evaluate side-chains 181 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 100 optimal weight: 0.0970 chunk 99 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 116 optimal weight: 0.0770 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.200013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165654 restraints weight = 2494.293| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 0.67 r_work: 0.3680 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9417 Z= 0.117 Angle : 0.483 6.414 12783 Z= 0.251 Chirality : 0.038 0.132 1626 Planarity : 0.003 0.032 1557 Dihedral : 4.633 54.199 1287 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.36 % Allowed : 24.04 % Favored : 72.60 % 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: 1.71 (0.23), residues: 1200 helix: 1.74 (0.16), residues: 900 sheet: -0.01 (0.62), residues: 48 loop : -0.81 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 353 TYR 0.010 0.001 TYR A 162 PHE 0.011 0.001 PHE C 240 TRP 0.011 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9417) covalent geometry : angle 0.48302 / 0.25 (12783) hydrogen bonds : bond 0.03712 / 2.55 ( 726) hydrogen bonds : angle 4.32593 / 3.13 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.261 Fit side-chains REVERT: A 99 PHE cc_start: 0.7641 (t80) cc_final: 0.7125 (t80) REVERT: A 117 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7602 (mttp) REVERT: A 138 THR cc_start: 0.6884 (OUTLIER) cc_final: 0.6501 (m) REVERT: A 277 GLU cc_start: 0.6389 (tm-30) cc_final: 0.6180 (mp0) REVERT: A 303 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7603 (tp) REVERT: A 315 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7214 (ttm110) REVERT: A 356 ARG cc_start: 0.6987 (mmt180) cc_final: 0.6693 (mmt180) REVERT: A 444 ASP cc_start: 0.7911 (t0) cc_final: 0.7577 (t70) REVERT: B 68 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7293 (tp) REVERT: B 138 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6563 (m) REVERT: B 205 MET cc_start: 0.8097 (ptt) cc_final: 0.7889 (ptm) REVERT: B 228 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7496 (mmtm) REVERT: B 258 MET cc_start: 0.8395 (tpp) cc_final: 0.8140 (tpt) REVERT: B 277 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6358 (pm20) REVERT: B 315 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7313 (ttm170) REVERT: B 445 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7419 (mmt180) REVERT: C 68 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7208 (tp) REVERT: C 138 THR cc_start: 0.6900 (OUTLIER) cc_final: 0.6485 (m) REVERT: C 205 MET cc_start: 0.8096 (ptt) cc_final: 0.7785 (ptm) REVERT: C 228 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7399 (mtmt) REVERT: C 235 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7931 (tt) REVERT: C 304 ILE cc_start: 0.7799 (tt) cc_final: 0.7520 (mt) REVERT: C 315 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7395 (ttm110) REVERT: C 357 PHE cc_start: 0.7795 (t80) cc_final: 0.7561 (t80) REVERT: C 419 MET cc_start: 0.8840 (mmm) cc_final: 0.8491 (tpp) REVERT: C 444 ASP cc_start: 0.7968 (t0) cc_final: 0.7669 (t70) outliers start: 34 outliers final: 12 residues processed: 189 average time/residue: 0.4862 time to fit residues: 98.8295 Evaluate side-chains 178 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.195544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159518 restraints weight = 2872.506| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 0.74 r_work: 0.3610 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9417 Z= 0.148 Angle : 0.526 6.306 12783 Z= 0.271 Chirality : 0.040 0.134 1626 Planarity : 0.004 0.033 1557 Dihedral : 4.094 37.115 1287 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.66 % Allowed : 23.15 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.23), residues: 1200 helix: 1.44 (0.16), residues: 936 sheet: -0.10 (0.64), residues: 48 loop : -1.07 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 445 TYR 0.010 0.001 TYR B 162 PHE 0.016 0.002 PHE B 240 TRP 0.012 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9417) covalent geometry : angle 0.52602 / 0.27 (12783) hydrogen bonds : bond 0.04156 / 2.86 ( 726) hydrogen bonds : angle 4.43540 / 3.21 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.344 Fit side-chains REVERT: A 99 PHE cc_start: 0.7762 (t80) cc_final: 0.7308 (t80) REVERT: A 117 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7582 (mttp) REVERT: A 138 THR cc_start: 0.6755 (OUTLIER) cc_final: 0.6425 (m) REVERT: A 167 GLU cc_start: 0.7488 (pp20) cc_final: 0.7105 (pp20) REVERT: A 277 GLU cc_start: 0.6367 (tm-30) cc_final: 0.6077 (mp0) REVERT: A 303 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7591 (tp) REVERT: A 315 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7300 (ttm110) REVERT: A 356 ARG cc_start: 0.6994 (mmt180) cc_final: 0.6678 (mmt180) REVERT: A 444 ASP cc_start: 0.7992 (t0) cc_final: 0.7697 (t70) REVERT: B 68 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7244 (tp) REVERT: B 138 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6632 (m) REVERT: B 167 GLU cc_start: 0.7738 (pp20) cc_final: 0.7364 (pp20) REVERT: B 168 GLU cc_start: 0.5725 (tp30) cc_final: 0.4860 (tp30) REVERT: B 228 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7540 (mmtm) REVERT: B 258 MET cc_start: 0.8435 (tpp) cc_final: 0.8156 (tpt) REVERT: B 277 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6424 (pm20) REVERT: B 315 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7268 (ttm170) REVERT: B 445 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.6821 (mtt90) REVERT: C 68 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7193 (tp) REVERT: C 117 LYS cc_start: 0.8256 (mtmm) cc_final: 0.6506 (tmtt) REVERT: C 138 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6490 (m) REVERT: C 167 GLU cc_start: 0.7318 (pp20) cc_final: 0.7062 (pp20) REVERT: C 205 MET cc_start: 0.8232 (ptt) cc_final: 0.7993 (ptm) REVERT: C 228 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7456 (mtmt) REVERT: C 304 ILE cc_start: 0.7776 (tt) cc_final: 0.7525 (mt) REVERT: C 315 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7370 (ttm110) REVERT: C 357 PHE cc_start: 0.7867 (t80) cc_final: 0.7620 (t80) REVERT: C 419 MET cc_start: 0.8870 (mmm) cc_final: 0.8540 (tpp) REVERT: C 444 ASP cc_start: 0.8015 (t0) cc_final: 0.7780 (t70) outliers start: 37 outliers final: 13 residues processed: 197 average time/residue: 0.5625 time to fit residues: 118.4297 Evaluate side-chains 178 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.196180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.160125 restraints weight = 3148.247| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 0.78 r_work: 0.3618 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9417 Z= 0.132 Angle : 0.508 5.910 12783 Z= 0.261 Chirality : 0.039 0.134 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.943 34.045 1287 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.36 % Allowed : 23.64 % Favored : 73.00 % 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: 1.52 (0.23), residues: 1200 helix: 1.58 (0.16), residues: 924 sheet: -0.22 (0.64), residues: 48 loop : -0.98 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 353 TYR 0.009 0.001 TYR B 162 PHE 0.013 0.002 PHE C 240 TRP 0.014 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9417) covalent geometry : angle 0.50818 / 0.26 (12783) hydrogen bonds : bond 0.03924 / 2.70 ( 726) hydrogen bonds : angle 4.35864 / 3.16 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7748 (t80) cc_final: 0.7289 (t80) REVERT: A 117 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7578 (mttp) REVERT: A 138 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6391 (m) REVERT: A 167 GLU cc_start: 0.7477 (pp20) cc_final: 0.7030 (pp20) REVERT: A 272 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6897 (mp0) REVERT: A 277 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6336 (mp0) REVERT: A 303 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7595 (tp) REVERT: A 315 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7266 (ttm110) REVERT: A 356 ARG cc_start: 0.7006 (mmt180) cc_final: 0.6678 (mmt180) REVERT: A 444 ASP cc_start: 0.7938 (t0) cc_final: 0.7631 (t70) REVERT: B 68 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7290 (tp) REVERT: B 99 PHE cc_start: 0.7734 (t80) cc_final: 0.7417 (t80) REVERT: B 138 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6632 (m) REVERT: B 167 GLU cc_start: 0.7687 (pp20) cc_final: 0.7325 (pp20) REVERT: B 168 GLU cc_start: 0.5658 (tp30) cc_final: 0.4898 (tp30) REVERT: B 228 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7584 (mmtm) REVERT: B 258 MET cc_start: 0.8450 (tpp) cc_final: 0.8166 (tpt) REVERT: B 277 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6388 (pm20) REVERT: B 306 PHE cc_start: 0.7459 (t80) cc_final: 0.7234 (t80) REVERT: B 315 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7284 (ttm170) REVERT: B 440 ASP cc_start: 0.7775 (t70) cc_final: 0.7487 (t0) REVERT: B 445 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6826 (mtt90) REVERT: C 68 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7189 (tp) REVERT: C 117 LYS cc_start: 0.8271 (mtmm) cc_final: 0.6513 (tmtt) REVERT: C 205 MET cc_start: 0.8266 (ptt) cc_final: 0.7924 (ptm) REVERT: C 228 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7519 (mmtm) REVERT: C 277 GLU cc_start: 0.6413 (tm-30) cc_final: 0.6110 (pm20) REVERT: C 304 ILE cc_start: 0.7774 (tt) cc_final: 0.7464 (mt) REVERT: C 315 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7390 (ttm110) REVERT: C 419 MET cc_start: 0.8915 (mmm) cc_final: 0.8698 (mmm) REVERT: C 444 ASP cc_start: 0.8004 (t0) cc_final: 0.7741 (t70) outliers start: 34 outliers final: 12 residues processed: 190 average time/residue: 0.5061 time to fit residues: 102.8402 Evaluate side-chains 183 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.194222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159305 restraints weight = 2889.333| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 0.73 r_work: 0.3611 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9417 Z= 0.155 Angle : 0.540 5.592 12783 Z= 0.276 Chirality : 0.040 0.153 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.983 32.597 1287 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.77 % Allowed : 24.13 % Favored : 73.10 % 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: 1.36 (0.23), residues: 1200 helix: 1.49 (0.16), residues: 921 sheet: -0.31 (0.65), residues: 48 loop : -1.10 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.010 0.001 TYR B 162 PHE 0.016 0.002 PHE C 240 TRP 0.016 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 9417) covalent geometry : angle 0.54046 / 0.28 (12783) hydrogen bonds : bond 0.04179 / 2.88 ( 726) hydrogen bonds : angle 4.46059 / 3.23 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7881 (t80) cc_final: 0.7411 (t80) REVERT: A 117 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7621 (mttp) REVERT: A 138 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6432 (m) REVERT: A 167 GLU cc_start: 0.7467 (pp20) cc_final: 0.6952 (pp20) REVERT: A 272 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6887 (mp0) REVERT: A 277 GLU cc_start: 0.6400 (tm-30) cc_final: 0.6111 (mp0) REVERT: A 303 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7440 (tp) REVERT: A 315 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7336 (ttm110) REVERT: A 444 ASP cc_start: 0.8004 (t0) cc_final: 0.7733 (t70) REVERT: B 68 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7268 (tp) REVERT: B 99 PHE cc_start: 0.7813 (t80) cc_final: 0.7454 (t80) REVERT: B 138 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6638 (m) REVERT: B 167 GLU cc_start: 0.7670 (pp20) cc_final: 0.7297 (pp20) REVERT: B 168 GLU cc_start: 0.5851 (tp30) cc_final: 0.5157 (tp30) REVERT: B 228 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7653 (mmtm) REVERT: B 258 MET cc_start: 0.8442 (tpp) cc_final: 0.8174 (tpt) REVERT: B 277 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6510 (pm20) REVERT: B 315 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7286 (ttm170) REVERT: B 440 ASP cc_start: 0.7841 (t70) cc_final: 0.7555 (t70) REVERT: B 445 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7817 (mtt90) REVERT: C 68 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7180 (tp) REVERT: C 117 LYS cc_start: 0.8291 (mtmm) cc_final: 0.6545 (tmtt) REVERT: C 205 MET cc_start: 0.8274 (ptt) cc_final: 0.7940 (ptm) REVERT: C 228 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7607 (mmtm) REVERT: C 277 GLU cc_start: 0.6435 (tm-30) cc_final: 0.6181 (pm20) REVERT: C 304 ILE cc_start: 0.7804 (tt) cc_final: 0.7529 (mt) REVERT: C 315 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7420 (ttm110) REVERT: C 357 PHE cc_start: 0.7863 (t80) cc_final: 0.7644 (t80) REVERT: C 419 MET cc_start: 0.8955 (mmm) cc_final: 0.8693 (tpp) REVERT: C 444 ASP cc_start: 0.8038 (t0) cc_final: 0.7817 (t70) outliers start: 28 outliers final: 14 residues processed: 177 average time/residue: 0.4998 time to fit residues: 94.5494 Evaluate side-chains 177 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.0050 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 0.0370 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.192557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.160904 restraints weight = 2670.751| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 0.58 r_work: 0.3459 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9417 Z= 0.127 Angle : 0.511 6.017 12783 Z= 0.261 Chirality : 0.039 0.147 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.862 31.186 1287 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.47 % Allowed : 24.43 % Favored : 73.10 % 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: 1.48 (0.23), residues: 1200 helix: 1.58 (0.16), residues: 921 sheet: -0.44 (0.64), residues: 48 loop : -1.08 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.011 0.001 TYR B 162 PHE 0.013 0.001 PHE C 240 TRP 0.018 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9417) covalent geometry : angle 0.51147 / 0.26 (12783) hydrogen bonds : bond 0.03850 / 2.66 ( 726) hydrogen bonds : angle 4.36174 / 3.16 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7807 (t80) cc_final: 0.7419 (t80) REVERT: A 117 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7647 (mttp) REVERT: A 167 GLU cc_start: 0.7406 (pp20) cc_final: 0.6981 (pp20) REVERT: A 272 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6907 (mp0) REVERT: A 277 GLU cc_start: 0.6647 (tm-30) cc_final: 0.6396 (mp0) REVERT: A 303 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7603 (tp) REVERT: A 315 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7377 (ttm110) REVERT: A 444 ASP cc_start: 0.7909 (t0) cc_final: 0.7609 (t70) REVERT: B 68 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7392 (tp) REVERT: B 99 PHE cc_start: 0.7745 (t80) cc_final: 0.7451 (t80) REVERT: B 114 VAL cc_start: 0.8071 (t) cc_final: 0.7854 (m) REVERT: B 167 GLU cc_start: 0.7673 (pp20) cc_final: 0.7352 (pp20) REVERT: B 228 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7701 (mmtm) REVERT: B 258 MET cc_start: 0.8399 (tpp) cc_final: 0.8115 (tpt) REVERT: B 303 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7801 (tt) REVERT: B 315 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7337 (ttm170) REVERT: B 440 ASP cc_start: 0.7859 (t70) cc_final: 0.7568 (t0) REVERT: B 445 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7496 (mmt180) REVERT: C 68 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7379 (tp) REVERT: C 117 LYS cc_start: 0.8301 (mtmm) cc_final: 0.6609 (tmtt) REVERT: C 205 MET cc_start: 0.8220 (ptt) cc_final: 0.7912 (ptm) REVERT: C 228 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7745 (mmtm) REVERT: C 277 GLU cc_start: 0.6419 (tm-30) cc_final: 0.6197 (pm20) REVERT: C 304 ILE cc_start: 0.7907 (tt) cc_final: 0.7614 (mt) REVERT: C 315 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7447 (ttm110) REVERT: C 419 MET cc_start: 0.8956 (mmm) cc_final: 0.8717 (tpp) REVERT: C 444 ASP cc_start: 0.7966 (t0) cc_final: 0.7704 (t70) outliers start: 25 outliers final: 15 residues processed: 180 average time/residue: 0.5154 time to fit residues: 99.2305 Evaluate side-chains 177 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 112 optimal weight: 0.0050 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.192669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.160002 restraints weight = 3033.700| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 0.64 r_work: 0.3509 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9417 Z= 0.123 Angle : 0.515 6.782 12783 Z= 0.263 Chirality : 0.039 0.144 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.785 29.449 1287 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.08 % Allowed : 25.12 % Favored : 72.80 % 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: 1.59 (0.23), residues: 1200 helix: 1.67 (0.16), residues: 921 sheet: -0.42 (0.65), residues: 48 loop : -1.05 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.011 0.001 TYR B 162 PHE 0.012 0.001 PHE C 240 TRP 0.017 0.001 TRP A 256 HIS 0.002 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9417) covalent geometry : angle 0.51517 / 0.26 (12783) hydrogen bonds : bond 0.03788 / 2.62 ( 726) hydrogen bonds : angle 4.32787 / 3.14 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7789 (t80) cc_final: 0.7377 (t80) REVERT: A 117 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7621 (mttp) REVERT: A 167 GLU cc_start: 0.7372 (pp20) cc_final: 0.6942 (pp20) REVERT: A 272 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6883 (mp0) REVERT: A 277 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6345 (mp0) REVERT: A 303 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 315 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7346 (ttm110) REVERT: A 444 ASP cc_start: 0.7886 (t0) cc_final: 0.7576 (t70) REVERT: B 68 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7455 (tp) REVERT: B 99 PHE cc_start: 0.7754 (t80) cc_final: 0.7467 (t80) REVERT: B 114 VAL cc_start: 0.8036 (t) cc_final: 0.7793 (m) REVERT: B 167 GLU cc_start: 0.7649 (pp20) cc_final: 0.7313 (pp20) REVERT: B 228 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7681 (mmtm) REVERT: B 258 MET cc_start: 0.8418 (tpp) cc_final: 0.8134 (tpt) REVERT: B 277 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6457 (pm20) REVERT: B 303 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7684 (tt) REVERT: B 315 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7318 (ttm170) REVERT: B 419 MET cc_start: 0.8609 (tpt) cc_final: 0.8203 (mmt) REVERT: B 440 ASP cc_start: 0.7827 (t70) cc_final: 0.7530 (t70) REVERT: B 445 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7479 (mmt180) REVERT: C 22 LEU cc_start: 0.8255 (mp) cc_final: 0.7909 (mt) REVERT: C 68 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7360 (tp) REVERT: C 117 LYS cc_start: 0.8273 (mtmm) cc_final: 0.6555 (tmtt) REVERT: C 205 MET cc_start: 0.8233 (ptt) cc_final: 0.7927 (ptm) REVERT: C 228 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7566 (mtmt) REVERT: C 304 ILE cc_start: 0.7874 (tt) cc_final: 0.7546 (mt) REVERT: C 315 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7404 (ttm110) REVERT: C 357 PHE cc_start: 0.7942 (t80) cc_final: 0.7727 (t80) REVERT: C 419 MET cc_start: 0.8958 (mmm) cc_final: 0.8596 (tpp) REVERT: C 444 ASP cc_start: 0.7968 (t0) cc_final: 0.7702 (t70) outliers start: 21 outliers final: 11 residues processed: 177 average time/residue: 0.5706 time to fit residues: 108.0320 Evaluate side-chains 174 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.190266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156900 restraints weight = 3168.876| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 0.67 r_work: 0.3509 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9417 Z= 0.144 Angle : 0.545 8.673 12783 Z= 0.277 Chirality : 0.040 0.146 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.884 29.790 1287 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.27 % Allowed : 24.83 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.23), residues: 1200 helix: 1.63 (0.16), residues: 921 sheet: -0.38 (0.65), residues: 48 loop : -1.09 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 445 TYR 0.011 0.001 TYR B 162 PHE 0.015 0.002 PHE B 240 TRP 0.021 0.002 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 9417) covalent geometry : angle 0.54496 / 0.28 (12783) hydrogen bonds : bond 0.04035 / 2.79 ( 726) hydrogen bonds : angle 4.39346 / 3.19 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3144.45 seconds wall clock time: 54 minutes 15.26 seconds (3255.26 seconds total)