Starting phenix.real_space_refine on Wed Sep 17 21:35:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zxp_60548/09_2025/8zxp_60548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zxp_60548/09_2025/8zxp_60548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zxp_60548/09_2025/8zxp_60548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zxp_60548/09_2025/8zxp_60548.map" model { file = "/net/cci-nas-00/data/ceres_data/8zxp_60548/09_2025/8zxp_60548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zxp_60548/09_2025/8zxp_60548.cif" } resolution = 3.09 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= 0.004 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7806 2.51 5 N 1779 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3858 Classifications: {'peptide': 494} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 474} Chain: "B" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3858 Classifications: {'peptide': 494} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 473} Chain: "C" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3858 Classifications: {'peptide': 494} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 474} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.90, per 1000 atoms: 0.25 Number of scatterers: 11586 At special positions: 0 Unit cell: (116.6, 115.54, 78.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1953 8.00 N 1779 7.00 C 7806 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 500.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 83.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 15 through 34 removed outlier: 4.227A pdb=" N ILE A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.583A pdb=" N TRP A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 6.272A pdb=" N TRP A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.513A pdb=" N ARG A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 80 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.830A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 103 " --> pdb=" O MET A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.549A pdb=" N ALA A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 167 removed outlier: 3.504A pdb=" N TRP A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 153 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.961A pdb=" N PHE A 178 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 179' Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.982A pdb=" N HIS A 187 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 216 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.577A pdb=" N ILE A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 279 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.528A pdb=" N THR A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.547A pdb=" N VAL A 333 " --> pdb=" O TRP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 379 removed outlier: 4.925A pdb=" N VAL A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Proline residue: A 357 - end of helix removed outlier: 3.922A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.140A pdb=" N ASN A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 435 removed outlier: 3.584A pdb=" N SER A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 464 Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.973A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 501 removed outlier: 3.588A pdb=" N ALA A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 34 removed outlier: 4.036A pdb=" N ILE B 19 " --> pdb=" O PRO B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 74 Proline residue: B 44 - end of helix removed outlier: 6.138A pdb=" N TRP B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.655A pdb=" N ILE B 80 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.608A pdb=" N THR B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.575A pdb=" N TRP B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 153 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.889A pdb=" N HIS B 187 " --> pdb=" O GLU B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 191 through 226 Processing helix chain 'B' and resid 230 through 250 Processing helix chain 'B' and resid 258 through 279 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 313 through 318 removed outlier: 4.221A pdb=" N VAL B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 345 through 379 removed outlier: 4.947A pdb=" N VAL B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Proline residue: B 357 - end of helix removed outlier: 3.911A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.595A pdb=" N ALA B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.703A pdb=" N ASN B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 437 removed outlier: 3.561A pdb=" N SER B 423 " --> pdb=" O PHE B 419 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 464 removed outlier: 3.715A pdb=" N PHE B 449 " --> pdb=" O TRP B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 479 removed outlier: 4.054A pdb=" N LEU B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 501 removed outlier: 3.528A pdb=" N ALA B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 38 through 74 removed outlier: 3.681A pdb=" N TRP C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Proline residue: C 44 - end of helix removed outlier: 6.196A pdb=" N TRP C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.572A pdb=" N ARG C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 80 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 104 removed outlier: 3.676A pdb=" N ALA C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 103 " --> pdb=" O MET C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.548A pdb=" N PHE C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'C' and resid 147 through 167 removed outlier: 3.664A pdb=" N TRP C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE C 153 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 187 removed outlier: 3.923A pdb=" N HIS C 187 " --> pdb=" O GLU C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 187' Processing helix chain 'C' and resid 191 through 226 Processing helix chain 'C' and resid 232 through 250 removed outlier: 3.721A pdb=" N GLY C 236 " --> pdb=" O MET C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 279 Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.567A pdb=" N THR C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 345 through 379 removed outlier: 4.950A pdb=" N VAL C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Proline residue: C 357 - end of helix removed outlier: 3.894A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.864A pdb=" N ASN C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 437 removed outlier: 3.565A pdb=" N SER C 423 " --> pdb=" O PHE C 419 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 464 Processing helix chain 'C' and resid 466 through 479 removed outlier: 4.110A pdb=" N LEU C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 503 854 hydrogen bonds defined for protein. 2547 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: 1.74 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3313 1.34 - 1.46: 2892 1.46 - 1.58: 5645 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11940 Sorted by residual: bond pdb=" C SER C 230 " pdb=" N PRO C 231 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.37e+00 bond pdb=" CA VAL A 444 " pdb=" CB VAL A 444 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.05e-02 9.07e+03 3.93e+00 bond pdb=" CB GLU C 184 " pdb=" CG GLU C 184 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB TRP C 323 " pdb=" CG TRP C 323 " ideal model delta sigma weight residual 1.498 1.554 -0.056 3.10e-02 1.04e+03 3.21e+00 bond pdb=" CB TRP A 323 " pdb=" CG TRP A 323 " ideal model delta sigma weight residual 1.498 1.550 -0.052 3.10e-02 1.04e+03 2.84e+00 ... (remaining 11935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 15949 2.82 - 5.64: 266 5.64 - 8.46: 61 8.46 - 11.28: 14 11.28 - 14.09: 3 Bond angle restraints: 16293 Sorted by residual: angle pdb=" N TRP B 445 " pdb=" CA TRP B 445 " pdb=" C TRP B 445 " ideal model delta sigma weight residual 114.62 107.58 7.04 1.14e+00 7.69e-01 3.81e+01 angle pdb=" C GLY C 106 " pdb=" N ILE C 107 " pdb=" CA ILE C 107 " ideal model delta sigma weight residual 121.70 132.21 -10.51 1.80e+00 3.09e-01 3.41e+01 angle pdb=" C GLU C 441 " pdb=" N SER C 442 " pdb=" CA SER C 442 " ideal model delta sigma weight residual 121.70 131.96 -10.26 1.80e+00 3.09e-01 3.25e+01 angle pdb=" C GLY B 256 " pdb=" N VAL B 257 " pdb=" CA VAL B 257 " ideal model delta sigma weight residual 121.70 131.74 -10.04 1.80e+00 3.09e-01 3.11e+01 angle pdb=" CA ILE B 19 " pdb=" CB ILE B 19 " pdb=" CG1 ILE B 19 " ideal model delta sigma weight residual 110.40 118.67 -8.27 1.70e+00 3.46e-01 2.37e+01 ... (remaining 16288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 5579 17.12 - 34.25: 815 34.25 - 51.37: 215 51.37 - 68.50: 34 68.50 - 85.62: 5 Dihedral angle restraints: 6648 sinusoidal: 2442 harmonic: 4206 Sorted by residual: dihedral pdb=" CA ASN C 14 " pdb=" C ASN C 14 " pdb=" N PRO C 15 " pdb=" CA PRO C 15 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN B 14 " pdb=" C ASN B 14 " pdb=" N PRO B 15 " pdb=" CA PRO B 15 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASN A 14 " pdb=" C ASN A 14 " pdb=" N PRO A 15 " pdb=" CA PRO A 15 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 6645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1531 0.063 - 0.126: 287 0.126 - 0.188: 56 0.188 - 0.251: 6 0.251 - 0.314: 1 Chirality restraints: 1881 Sorted by residual: chirality pdb=" CB THR A 472 " pdb=" CA THR A 472 " pdb=" OG1 THR A 472 " pdb=" CG2 THR A 472 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE A 229 " pdb=" CA ILE A 229 " pdb=" CG1 ILE A 229 " pdb=" CG2 ILE A 229 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A 109 " pdb=" CA ILE A 109 " pdb=" CG1 ILE A 109 " pdb=" CG2 ILE A 109 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1878 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 444 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C VAL B 444 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL B 444 " -0.022 2.00e-02 2.50e+03 pdb=" N TRP B 445 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 230 " 0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO A 231 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 444 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C VAL A 444 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL A 444 " -0.021 2.00e-02 2.50e+03 pdb=" N TRP A 445 " -0.018 2.00e-02 2.50e+03 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3432 2.82 - 3.34: 10813 3.34 - 3.86: 20371 3.86 - 4.38: 21995 4.38 - 4.90: 40265 Nonbonded interactions: 96876 Sorted by model distance: nonbonded pdb=" OG SER C 248 " pdb=" O LYS C 255 " model vdw 2.297 3.040 nonbonded pdb=" O THR A 103 " pdb=" OG1 THR A 103 " model vdw 2.303 3.040 nonbonded pdb=" O ALA A 27 " pdb=" OG1 THR A 31 " model vdw 2.304 3.040 nonbonded pdb=" O ALA C 27 " pdb=" OG1 THR C 31 " model vdw 2.312 3.040 nonbonded pdb=" O GLY C 313 " pdb=" ND2 ASN C 316 " model vdw 2.342 3.120 ... (remaining 96871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.010 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.005 0.067 11941 Z= 0.234 Angle : 0.984 14.094 16293 Z= 0.537 Chirality : 0.052 0.314 1881 Planarity : 0.007 0.104 1962 Dihedral : 16.926 85.619 3954 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.41 % Allowed : 29.32 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -1.54 (0.18), residues: 1476 helix: -0.64 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 81 TYR 0.013 0.001 TYR A 154 PHE 0.041 0.002 PHE C 420 TRP 0.040 0.003 TRP C 329 HIS 0.008 0.002 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00487 (11940) covalent geometry : angle 0.98370 (16293) hydrogen bonds : bond 0.11536 ( 854) hydrogen bonds : angle 6.47912 ( 2547) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 LEU cc_start: 0.7432 (tp) cc_final: 0.7111 (mp) REVERT: A 481 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: B 332 PHE cc_start: 0.8263 (t80) cc_final: 0.7793 (t80) REVERT: C 140 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: C 168 ARG cc_start: 0.8533 (mmt-90) cc_final: 0.8114 (mpt180) outliers start: 5 outliers final: 1 residues processed: 164 average time/residue: 0.1041 time to fit residues: 24.5477 Evaluate side-chains 154 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain C residue 140 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111698 restraints weight = 15128.732| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.15 r_work: 0.3153 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11941 Z= 0.135 Angle : 0.558 7.731 16293 Z= 0.296 Chirality : 0.039 0.166 1881 Planarity : 0.004 0.073 1962 Dihedral : 4.950 57.328 1545 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 3.03 % Allowed : 25.31 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 0.67 (0.21), residues: 1476 helix: 1.08 (0.15), residues: 1095 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 81 TYR 0.018 0.001 TYR C 154 PHE 0.027 0.001 PHE B 420 TRP 0.016 0.001 TRP C 329 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00304 (11940) covalent geometry : angle 0.55850 (16293) hydrogen bonds : bond 0.03928 ( 854) hydrogen bonds : angle 4.49368 ( 2547) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.6789 (ttm110) cc_final: 0.6556 (ttp-110) REVERT: A 447 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7497 (mmm-85) REVERT: A 481 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: B 185 ARG cc_start: 0.7187 (ttp-110) cc_final: 0.6729 (mtp85) REVERT: B 332 PHE cc_start: 0.8333 (t80) cc_final: 0.8122 (t80) REVERT: B 429 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7294 (tt) REVERT: B 481 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 488 MET cc_start: 0.8063 (tmm) cc_final: 0.7630 (ttp) REVERT: C 38 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6611 (tppt) REVERT: C 156 MET cc_start: 0.7999 (mmm) cc_final: 0.7639 (mmm) REVERT: C 316 ASN cc_start: 0.8946 (p0) cc_final: 0.8742 (p0) REVERT: C 481 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7973 (m-80) outliers start: 37 outliers final: 19 residues processed: 192 average time/residue: 0.0962 time to fit residues: 26.4824 Evaluate side-chains 179 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 484 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109632 restraints weight = 15099.115| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.10 r_work: 0.3117 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11941 Z= 0.138 Angle : 0.547 6.393 16293 Z= 0.286 Chirality : 0.040 0.172 1881 Planarity : 0.004 0.072 1962 Dihedral : 4.666 59.199 1541 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 4.34 % Allowed : 25.80 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.44 (0.22), residues: 1476 helix: 1.64 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -1.05 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 81 TYR 0.009 0.001 TYR B 295 PHE 0.024 0.001 PHE B 420 TRP 0.014 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00318 (11940) covalent geometry : angle 0.54711 (16293) hydrogen bonds : bond 0.03845 ( 854) hydrogen bonds : angle 4.22737 ( 2547) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.6771 (ttm110) cc_final: 0.6506 (ttp-110) REVERT: A 262 ASN cc_start: 0.6827 (OUTLIER) cc_final: 0.6406 (t0) REVERT: A 447 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7637 (mmm160) REVERT: A 481 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: B 131 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7233 (t0) REVERT: B 185 ARG cc_start: 0.7089 (ttp-110) cc_final: 0.6602 (mtp85) REVERT: B 351 LEU cc_start: 0.7824 (mm) cc_final: 0.7615 (mm) REVERT: B 481 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: B 488 MET cc_start: 0.8159 (tmm) cc_final: 0.7953 (ttp) REVERT: C 38 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6620 (tppt) REVERT: C 91 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6566 (t80) REVERT: C 316 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (p0) REVERT: C 481 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: C 499 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7535 (tp30) outliers start: 53 outliers final: 21 residues processed: 196 average time/residue: 0.1017 time to fit residues: 28.7592 Evaluate side-chains 182 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111016 restraints weight = 15128.044| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.09 r_work: 0.3145 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11941 Z= 0.126 Angle : 0.532 6.417 16293 Z= 0.278 Chirality : 0.039 0.166 1881 Planarity : 0.004 0.068 1962 Dihedral : 4.534 57.254 1541 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 4.18 % Allowed : 26.45 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.72 (0.22), residues: 1476 helix: 1.85 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -0.97 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.008 0.001 TYR B 295 PHE 0.022 0.001 PHE B 420 TRP 0.015 0.001 TRP B 329 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00286 (11940) covalent geometry : angle 0.53180 (16293) hydrogen bonds : bond 0.03705 ( 854) hydrogen bonds : angle 4.11348 ( 2547) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.6817 (ttm110) cc_final: 0.6561 (ttp-110) REVERT: A 447 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7388 (mmm160) REVERT: A 481 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: A 483 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7468 (p) REVERT: B 185 ARG cc_start: 0.7048 (ttp-110) cc_final: 0.6567 (mtp85) REVERT: B 429 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7441 (tt) REVERT: B 481 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: C 38 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6687 (tppt) REVERT: C 185 ARG cc_start: 0.7555 (ptm-80) cc_final: 0.7354 (ttp-110) REVERT: C 316 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8503 (m110) REVERT: C 481 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: C 499 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7577 (tp30) outliers start: 51 outliers final: 27 residues processed: 196 average time/residue: 0.0998 time to fit residues: 27.9755 Evaluate side-chains 192 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110258 restraints weight = 15052.350| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.16 r_work: 0.3113 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11941 Z= 0.139 Angle : 0.547 6.620 16293 Z= 0.285 Chirality : 0.040 0.163 1881 Planarity : 0.004 0.066 1962 Dihedral : 4.484 55.330 1541 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 4.18 % Allowed : 26.70 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.83 (0.22), residues: 1476 helix: 1.93 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -0.94 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.027 0.001 TYR C 154 PHE 0.029 0.001 PHE A 332 TRP 0.020 0.001 TRP B 329 HIS 0.002 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00324 (11940) covalent geometry : angle 0.54675 (16293) hydrogen bonds : bond 0.03766 ( 854) hydrogen bonds : angle 4.11091 ( 2547) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 42 TRP cc_start: 0.7359 (m-10) cc_final: 0.7150 (m-10) REVERT: A 185 ARG cc_start: 0.6894 (ttm110) cc_final: 0.6645 (ttp-110) REVERT: A 447 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7365 (mmm160) REVERT: A 481 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 483 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7475 (p) REVERT: B 99 MET cc_start: 0.8248 (ttt) cc_final: 0.7901 (ptm) REVERT: B 185 ARG cc_start: 0.7069 (ttp-110) cc_final: 0.6581 (mtp85) REVERT: B 429 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 481 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: C 38 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6641 (tppt) REVERT: C 91 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6856 (t80) REVERT: C 185 ARG cc_start: 0.7480 (ptm-80) cc_final: 0.7219 (ttp-110) REVERT: C 228 GLU cc_start: 0.6923 (pt0) cc_final: 0.6543 (pm20) REVERT: C 316 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8525 (m110) REVERT: C 481 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: C 499 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7582 (tp30) outliers start: 51 outliers final: 29 residues processed: 198 average time/residue: 0.1062 time to fit residues: 30.3645 Evaluate side-chains 195 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108169 restraints weight = 15158.673| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.16 r_work: 0.3111 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11941 Z= 0.142 Angle : 0.550 7.431 16293 Z= 0.286 Chirality : 0.040 0.165 1881 Planarity : 0.004 0.065 1962 Dihedral : 4.456 54.121 1541 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 4.18 % Allowed : 26.78 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.87 (0.22), residues: 1476 helix: 1.89 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -0.77 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 81 TYR 0.025 0.001 TYR C 154 PHE 0.030 0.001 PHE A 332 TRP 0.016 0.001 TRP B 329 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00335 (11940) covalent geometry : angle 0.54979 (16293) hydrogen bonds : bond 0.03774 ( 854) hydrogen bonds : angle 4.08613 ( 2547) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8903 (tp) cc_final: 0.8616 (mt) REVERT: A 42 TRP cc_start: 0.7351 (m-10) cc_final: 0.7127 (m-90) REVERT: A 185 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6760 (ttp-110) REVERT: A 195 ASP cc_start: 0.8485 (m-30) cc_final: 0.8187 (m-30) REVERT: A 447 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7415 (mmm160) REVERT: A 481 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: B 30 LEU cc_start: 0.8850 (tp) cc_final: 0.8573 (mp) REVERT: B 99 MET cc_start: 0.8247 (ttt) cc_final: 0.7916 (ptm) REVERT: B 185 ARG cc_start: 0.7073 (ttp-110) cc_final: 0.6578 (mtp85) REVERT: B 429 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7537 (tt) REVERT: B 481 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: C 38 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6616 (tppt) REVERT: C 91 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6668 (t80) REVERT: C 156 MET cc_start: 0.8006 (mmm) cc_final: 0.7665 (mmm) REVERT: C 185 ARG cc_start: 0.7489 (ptm-80) cc_final: 0.7282 (ttp-110) REVERT: C 316 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8506 (m110) REVERT: C 481 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: C 499 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7590 (tp30) outliers start: 51 outliers final: 33 residues processed: 199 average time/residue: 0.1091 time to fit residues: 31.1455 Evaluate side-chains 206 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 69 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109873 restraints weight = 14970.198| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.08 r_work: 0.3116 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11941 Z= 0.128 Angle : 0.537 7.081 16293 Z= 0.278 Chirality : 0.039 0.165 1881 Planarity : 0.004 0.062 1962 Dihedral : 4.398 52.831 1541 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 4.26 % Allowed : 26.78 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.93 (0.22), residues: 1476 helix: 1.96 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -0.85 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 81 TYR 0.024 0.001 TYR C 154 PHE 0.028 0.001 PHE A 332 TRP 0.023 0.001 TRP B 329 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00296 (11940) covalent geometry : angle 0.53680 (16293) hydrogen bonds : bond 0.03646 ( 854) hydrogen bonds : angle 4.04234 ( 2547) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8970 (tp) cc_final: 0.8633 (mt) REVERT: A 42 TRP cc_start: 0.7462 (m-10) cc_final: 0.7219 (m-90) REVERT: A 144 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 185 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6699 (ttp-110) REVERT: A 447 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7277 (mmm160) REVERT: A 481 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: A 483 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7469 (p) REVERT: B 30 LEU cc_start: 0.8851 (tp) cc_final: 0.8568 (mp) REVERT: B 99 MET cc_start: 0.8271 (ttt) cc_final: 0.7939 (ptm) REVERT: B 185 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6575 (mtp85) REVERT: B 218 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8460 (m) REVERT: B 429 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7475 (tt) REVERT: B 481 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: C 38 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6526 (tppt) REVERT: C 91 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6535 (t80) REVERT: C 185 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.7204 (ttp-110) REVERT: C 228 GLU cc_start: 0.6787 (pt0) cc_final: 0.6196 (pm20) REVERT: C 481 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: C 499 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7554 (tp30) outliers start: 52 outliers final: 35 residues processed: 194 average time/residue: 0.0987 time to fit residues: 27.7472 Evaluate side-chains 200 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 6 optimal weight: 0.0670 chunk 146 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110014 restraints weight = 15132.386| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.12 r_work: 0.3131 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11941 Z= 0.126 Angle : 0.539 8.307 16293 Z= 0.279 Chirality : 0.039 0.166 1881 Planarity : 0.004 0.062 1962 Dihedral : 4.331 51.682 1541 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 4.34 % Allowed : 26.45 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 2.00 (0.22), residues: 1476 helix: 2.01 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -0.85 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.024 0.001 TYR C 154 PHE 0.028 0.001 PHE A 332 TRP 0.021 0.001 TRP B 329 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00288 (11940) covalent geometry : angle 0.53890 (16293) hydrogen bonds : bond 0.03623 ( 854) hydrogen bonds : angle 4.00243 ( 2547) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8952 (tp) cc_final: 0.8643 (mt) REVERT: A 42 TRP cc_start: 0.7433 (m-10) cc_final: 0.7206 (m-90) REVERT: A 144 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8679 (tp) REVERT: A 195 ASP cc_start: 0.8441 (m-30) cc_final: 0.8132 (m-30) REVERT: A 447 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7246 (mmm160) REVERT: A 481 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: B 30 LEU cc_start: 0.8876 (tp) cc_final: 0.8588 (mp) REVERT: B 99 MET cc_start: 0.8243 (ttt) cc_final: 0.7925 (ptm) REVERT: B 185 ARG cc_start: 0.7086 (ttp-110) cc_final: 0.6601 (mtp85) REVERT: B 218 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 429 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 481 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: C 38 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6486 (tppt) REVERT: C 91 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6492 (t80) REVERT: C 185 ARG cc_start: 0.7409 (ptm-80) cc_final: 0.7190 (ttp-110) REVERT: C 228 GLU cc_start: 0.6795 (pt0) cc_final: 0.6245 (pm20) REVERT: C 481 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: C 499 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7575 (tp30) outliers start: 53 outliers final: 35 residues processed: 202 average time/residue: 0.1071 time to fit residues: 31.0244 Evaluate side-chains 204 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 85 optimal weight: 0.0030 chunk 112 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111477 restraints weight = 14812.290| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.12 r_work: 0.3143 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11941 Z= 0.118 Angle : 0.539 10.055 16293 Z= 0.277 Chirality : 0.039 0.167 1881 Planarity : 0.004 0.061 1962 Dihedral : 4.289 50.646 1541 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.10 % Allowed : 26.95 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 2.08 (0.22), residues: 1476 helix: 2.06 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -0.78 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 81 TYR 0.023 0.001 TYR C 154 PHE 0.040 0.001 PHE B 420 TRP 0.017 0.001 TRP B 329 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00265 (11940) covalent geometry : angle 0.53902 (16293) hydrogen bonds : bond 0.03515 ( 854) hydrogen bonds : angle 3.96504 ( 2547) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8951 (tp) cc_final: 0.8645 (mt) REVERT: A 42 TRP cc_start: 0.7397 (m-10) cc_final: 0.7192 (m-90) REVERT: A 144 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8650 (tp) REVERT: A 181 PHE cc_start: 0.7120 (t80) cc_final: 0.6558 (t80) REVERT: A 447 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7242 (mmm160) REVERT: A 481 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: A 483 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7456 (p) REVERT: B 30 LEU cc_start: 0.8871 (tp) cc_final: 0.8579 (mp) REVERT: B 99 MET cc_start: 0.8197 (ttt) cc_final: 0.7687 (ptm) REVERT: B 185 ARG cc_start: 0.7067 (ttp-110) cc_final: 0.6611 (mtp85) REVERT: B 218 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8484 (m) REVERT: B 429 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7469 (tt) REVERT: B 481 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: C 38 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6468 (tppt) REVERT: C 91 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6435 (t80) REVERT: C 228 GLU cc_start: 0.6876 (pt0) cc_final: 0.6307 (pm20) REVERT: C 481 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: C 499 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7605 (tp30) outliers start: 50 outliers final: 34 residues processed: 201 average time/residue: 0.1055 time to fit residues: 30.3686 Evaluate side-chains 209 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109470 restraints weight = 15172.618| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.14 r_work: 0.3132 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11941 Z= 0.131 Angle : 0.560 12.125 16293 Z= 0.286 Chirality : 0.040 0.165 1881 Planarity : 0.004 0.062 1962 Dihedral : 4.318 50.328 1541 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.77 % Allowed : 27.60 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 2.05 (0.22), residues: 1476 helix: 2.05 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -0.80 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 185 TYR 0.024 0.001 TYR C 154 PHE 0.038 0.001 PHE B 420 TRP 0.026 0.001 TRP B 329 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00305 (11940) covalent geometry : angle 0.55964 (16293) hydrogen bonds : bond 0.03628 ( 854) hydrogen bonds : angle 4.00537 ( 2547) Misc. bond : bond 0.00005 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8945 (tp) cc_final: 0.8641 (mt) REVERT: A 144 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8651 (tp) REVERT: A 181 PHE cc_start: 0.7154 (t80) cc_final: 0.6605 (t80) REVERT: A 227 TRP cc_start: 0.8146 (m-10) cc_final: 0.7861 (m-10) REVERT: B 30 LEU cc_start: 0.8856 (tp) cc_final: 0.8560 (mp) REVERT: B 99 MET cc_start: 0.8208 (ttt) cc_final: 0.7898 (ptm) REVERT: B 218 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8470 (m) REVERT: B 429 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7476 (tt) REVERT: B 481 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: C 38 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6498 (tppt) REVERT: C 91 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6454 (t80) REVERT: C 228 GLU cc_start: 0.6892 (pt0) cc_final: 0.6327 (pm20) REVERT: C 481 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: C 499 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7602 (tp30) outliers start: 46 outliers final: 36 residues processed: 194 average time/residue: 0.1054 time to fit residues: 29.8382 Evaluate side-chains 207 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 32 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 499 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 0.0060 chunk 66 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112309 restraints weight = 14972.509| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.12 r_work: 0.3157 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11941 Z= 0.116 Angle : 0.544 12.587 16293 Z= 0.278 Chirality : 0.039 0.168 1881 Planarity : 0.004 0.061 1962 Dihedral : 4.060 25.173 1539 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.52 % Allowed : 27.85 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 2.16 (0.22), residues: 1476 helix: 2.15 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -0.75 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 81 TYR 0.022 0.001 TYR C 154 PHE 0.036 0.001 PHE B 420 TRP 0.023 0.001 TRP B 329 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00259 (11940) covalent geometry : angle 0.54448 (16293) hydrogen bonds : bond 0.03469 ( 854) hydrogen bonds : angle 3.94392 ( 2547) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.23 seconds wall clock time: 42 minutes 9.37 seconds (2529.37 seconds total)