Starting phenix.real_space_refine on Sat Nov 16 16:36:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxp_60548/11_2024/8zxp_60548.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxp_60548/11_2024/8zxp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxp_60548/11_2024/8zxp_60548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxp_60548/11_2024/8zxp_60548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxp_60548/11_2024/8zxp_60548.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zxp_60548/11_2024/8zxp_60548.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 7.98, per 1000 atoms: 0.69 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: 2.86 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.13 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: 3.57 Time building geometry restraints manager: 3.23 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: 0.00 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.030 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- 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 11940 Z= 0.311 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (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 TRP 0.040 0.003 TRP C 329 HIS 0.008 0.002 HIS B 192 PHE 0.041 0.002 PHE C 420 TYR 0.013 0.001 TYR A 154 ARG 0.013 0.001 ARG A 81 *********************** 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 : 1.178 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: 0.2558 time to fit residues: 59.7423 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 : 1.284 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11940 Z= 0.198 Angle : 0.561 7.752 16293 Z= 0.297 Chirality : 0.039 0.167 1881 Planarity : 0.004 0.073 1962 Dihedral : 4.960 57.266 1545 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 3.11 % Allowed : 25.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1476 helix: 1.05 (0.15), residues: 1095 sheet: None (None), residues: 0 loop : -1.32 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 329 HIS 0.002 0.001 HIS A 149 PHE 0.028 0.001 PHE B 420 TYR 0.017 0.001 TYR C 154 ARG 0.005 0.001 ARG A 81 *********************** 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 202 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.6695 (ttm110) cc_final: 0.6478 (ttp-110) REVERT: A 447 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7570 (mmm-85) REVERT: A 481 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: B 185 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6630 (mtp85) REVERT: B 332 PHE cc_start: 0.8252 (t80) cc_final: 0.8013 (t80) REVERT: B 344 ARG cc_start: 0.8484 (mmt180) cc_final: 0.8133 (mmt180) REVERT: B 429 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7389 (tt) REVERT: B 481 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: B 488 MET cc_start: 0.8196 (tmm) cc_final: 0.7747 (ttp) REVERT: C 38 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6639 (tppt) REVERT: C 156 MET cc_start: 0.8160 (mmm) cc_final: 0.7842 (mmm) REVERT: C 481 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8122 (m-80) outliers start: 38 outliers final: 20 residues processed: 193 average time/residue: 0.2417 time to fit residues: 66.3932 Evaluate side-chains 179 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 64 VAL 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 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN C 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11940 Z= 0.203 Angle : 0.548 6.237 16293 Z= 0.287 Chirality : 0.040 0.172 1881 Planarity : 0.004 0.072 1962 Dihedral : 4.682 59.144 1541 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 4.26 % Allowed : 26.04 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.22), residues: 1476 helix: 1.61 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -1.09 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 PHE 0.024 0.001 PHE B 420 TYR 0.008 0.001 TYR B 295 ARG 0.003 0.000 ARG A 81 *********************** 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 215 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.6774 (ttm110) cc_final: 0.6518 (ttp-110) REVERT: A 262 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6650 (t0) REVERT: A 447 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7626 (mmm160) REVERT: A 481 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: B 131 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7326 (t0) REVERT: B 185 ARG cc_start: 0.7087 (ttp-110) cc_final: 0.6592 (mtp85) REVERT: B 481 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: B 488 MET cc_start: 0.8210 (tmm) cc_final: 0.7944 (ttp) REVERT: C 38 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6692 (tppt) REVERT: C 91 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6616 (t80) REVERT: C 481 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: C 499 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7545 (tp30) outliers start: 52 outliers final: 22 residues processed: 195 average time/residue: 0.2493 time to fit residues: 69.7908 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 : 1.186 ------------------------------------------------------------------------------- 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 308 THR 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 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 132 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11940 Z= 0.196 Angle : 0.539 6.443 16293 Z= 0.281 Chirality : 0.039 0.169 1881 Planarity : 0.004 0.068 1962 Dihedral : 4.567 57.207 1541 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 4.10 % Allowed : 26.62 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1476 helix: 1.81 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -1.00 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 PHE 0.022 0.001 PHE B 420 TYR 0.008 0.001 TYR B 295 ARG 0.002 0.000 ARG A 81 *********************** 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 214 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.6728 (ttm110) cc_final: 0.6484 (ttp-110) REVERT: A 447 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7405 (mmm160) REVERT: A 481 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: A 483 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7624 (p) REVERT: B 185 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6480 (mtp85) REVERT: B 429 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7483 (tt) REVERT: B 481 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: C 38 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6670 (tppt) REVERT: C 91 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6650 (t80) REVERT: C 481 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: C 499 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7538 (tp30) outliers start: 50 outliers final: 27 residues processed: 195 average time/residue: 0.2506 time to fit residues: 69.6519 Evaluate side-chains 190 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS 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 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 B residue 483 VAL 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 91 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 LEU 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 118 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 105 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11940 Z= 0.261 Angle : 0.570 6.823 16293 Z= 0.298 Chirality : 0.041 0.162 1881 Planarity : 0.004 0.067 1962 Dihedral : 4.589 56.064 1541 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 4.01 % Allowed : 26.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1476 helix: 1.77 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -0.93 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 329 HIS 0.002 0.001 HIS A 145 PHE 0.034 0.002 PHE A 332 TYR 0.011 0.001 TYR C 295 ARG 0.003 0.000 ARG B 81 *********************** 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: 49 poor density : 169 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 42 TRP cc_start: 0.7615 (m-10) cc_final: 0.7402 (m-90) REVERT: A 185 ARG cc_start: 0.6817 (ttm110) cc_final: 0.6565 (ttp-110) REVERT: A 447 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7431 (mmm160) REVERT: A 481 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: B 185 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6482 (mtp85) REVERT: B 429 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7592 (tt) REVERT: B 481 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: C 38 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6648 (tppt) REVERT: C 156 MET cc_start: 0.8190 (mmm) cc_final: 0.7952 (mmm) REVERT: C 481 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: C 499 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7557 (tp30) outliers start: 49 outliers final: 27 residues processed: 197 average time/residue: 0.2507 time to fit residues: 70.3618 Evaluate side-chains 191 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 483 VAL 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 100 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11940 Z= 0.273 Angle : 0.583 8.533 16293 Z= 0.303 Chirality : 0.041 0.171 1881 Planarity : 0.004 0.067 1962 Dihedral : 4.596 54.297 1541 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 4.59 % Allowed : 26.13 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1476 helix: 1.70 (0.16), residues: 1119 sheet: None (None), residues: 0 loop : -1.02 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 329 HIS 0.003 0.001 HIS B 192 PHE 0.028 0.002 PHE A 332 TYR 0.011 0.001 TYR C 295 ARG 0.003 0.000 ARG B 81 *********************** 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 226 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8949 (tp) cc_final: 0.8624 (mt) REVERT: A 42 TRP cc_start: 0.7688 (m-10) cc_final: 0.7443 (m-90) REVERT: A 185 ARG cc_start: 0.6891 (ttm110) cc_final: 0.6654 (ttp-110) REVERT: A 195 ASP cc_start: 0.8548 (m-30) cc_final: 0.8245 (m-30) REVERT: A 301 ASP cc_start: 0.8122 (t0) cc_final: 0.7838 (t0) REVERT: A 447 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7408 (mmm160) REVERT: A 481 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: B 30 LEU cc_start: 0.8853 (tp) cc_final: 0.8588 (mp) REVERT: B 185 ARG cc_start: 0.7050 (ttp-110) cc_final: 0.6562 (mtp85) REVERT: B 274 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8170 (mp) REVERT: B 429 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7666 (tt) REVERT: B 481 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: C 38 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6716 (tppt) REVERT: C 91 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6853 (t80) REVERT: C 481 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8311 (m-80) outliers start: 56 outliers final: 34 residues processed: 206 average time/residue: 0.2499 time to fit residues: 73.5054 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 : 1.381 ------------------------------------------------------------------------------- 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 95 SER Chi-restraints excluded: chain A residue 100 LEU 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 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 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 129 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 274 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 483 VAL 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.0970 chunk 81 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 119 optimal weight: 0.0370 chunk 79 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11940 Z= 0.167 Angle : 0.538 8.004 16293 Z= 0.278 Chirality : 0.039 0.166 1881 Planarity : 0.004 0.062 1962 Dihedral : 4.419 52.460 1541 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.10 % Allowed : 26.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.22), residues: 1476 helix: 1.98 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -0.95 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 329 HIS 0.002 0.001 HIS B 192 PHE 0.023 0.001 PHE A 332 TYR 0.007 0.001 TYR B 295 ARG 0.003 0.000 ARG B 81 *********************** 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 218 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8940 (tp) cc_final: 0.8646 (mt) REVERT: A 185 ARG cc_start: 0.6889 (ttm110) cc_final: 0.6657 (ttp-110) REVERT: A 447 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7295 (mmm160) REVERT: A 481 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: A 483 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7576 (p) REVERT: B 30 LEU cc_start: 0.8885 (tp) cc_final: 0.8611 (mp) REVERT: B 185 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6563 (mtp85) REVERT: B 218 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8519 (m) REVERT: B 429 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7605 (tt) REVERT: B 481 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: C 38 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6589 (tppt) REVERT: C 91 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6598 (t80) REVERT: C 481 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: C 499 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7642 (tp30) outliers start: 50 outliers final: 30 residues processed: 195 average time/residue: 0.2293 time to fit residues: 64.0511 Evaluate side-chains 199 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE 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 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 109 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 319 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 483 VAL 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 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 417 PHE 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 499 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11940 Z= 0.186 Angle : 0.552 9.370 16293 Z= 0.283 Chirality : 0.040 0.166 1881 Planarity : 0.004 0.062 1962 Dihedral : 4.386 51.528 1541 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 3.69 % Allowed : 27.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.22), residues: 1476 helix: 1.97 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 329 HIS 0.002 0.001 HIS B 192 PHE 0.025 0.001 PHE A 332 TYR 0.020 0.001 TYR C 154 ARG 0.005 0.000 ARG C 81 *********************** 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 205 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8940 (tp) cc_final: 0.8661 (mt) REVERT: A 185 ARG cc_start: 0.6879 (ttm110) cc_final: 0.6659 (ttp-110) REVERT: A 447 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7298 (mmm160) REVERT: A 481 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: B 30 LEU cc_start: 0.8861 (tp) cc_final: 0.8589 (mp) REVERT: B 99 MET cc_start: 0.8183 (ttt) cc_final: 0.7818 (ptm) REVERT: B 185 ARG cc_start: 0.7102 (ttp-110) cc_final: 0.6596 (mtp85) REVERT: B 218 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8528 (m) REVERT: B 429 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7601 (tt) REVERT: B 481 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: C 38 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6592 (tppt) REVERT: C 91 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6580 (t80) REVERT: C 481 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: C 499 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7617 (tp30) outliers start: 45 outliers final: 33 residues processed: 186 average time/residue: 0.2452 time to fit residues: 65.1742 Evaluate side-chains 198 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 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 109 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 319 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 483 VAL 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 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 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 123 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11940 Z= 0.255 Angle : 0.590 12.462 16293 Z= 0.303 Chirality : 0.041 0.165 1881 Planarity : 0.004 0.064 1962 Dihedral : 4.464 51.703 1541 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 3.60 % Allowed : 27.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.22), residues: 1476 helix: 1.87 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.91 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 329 HIS 0.003 0.001 HIS B 192 PHE 0.039 0.002 PHE B 420 TYR 0.025 0.002 TYR C 154 ARG 0.004 0.001 ARG A 81 *********************** 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 205 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8947 (tp) cc_final: 0.8667 (mt) REVERT: A 185 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6667 (ttp-110) REVERT: A 195 ASP cc_start: 0.8483 (m-30) cc_final: 0.8170 (m-30) REVERT: A 301 ASP cc_start: 0.8197 (t0) cc_final: 0.7927 (t0) REVERT: A 481 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 30 LEU cc_start: 0.8853 (tp) cc_final: 0.8576 (mp) REVERT: B 99 MET cc_start: 0.8171 (ttt) cc_final: 0.7795 (ptm) REVERT: B 185 ARG cc_start: 0.7111 (ttp-110) cc_final: 0.6599 (mtp85) REVERT: B 218 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8535 (m) REVERT: B 429 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7634 (tt) REVERT: B 481 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: C 38 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6700 (tppt) REVERT: C 91 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6509 (t80) REVERT: C 228 GLU cc_start: 0.6754 (pt0) cc_final: 0.6153 (pm20) REVERT: C 336 PHE cc_start: 0.7723 (t80) cc_final: 0.7515 (t80) REVERT: C 481 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: C 499 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7549 (tp30) outliers start: 44 outliers final: 31 residues processed: 189 average time/residue: 0.2413 time to fit residues: 65.6274 Evaluate side-chains 199 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 100 LEU 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 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 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 218 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 319 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 483 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ILE 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 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 139 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11940 Z= 0.212 Angle : 0.566 11.745 16293 Z= 0.292 Chirality : 0.040 0.166 1881 Planarity : 0.004 0.063 1962 Dihedral : 4.428 51.391 1541 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 3.60 % Allowed : 27.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1476 helix: 1.97 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -0.89 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 182 HIS 0.003 0.001 HIS B 192 PHE 0.040 0.001 PHE B 420 TYR 0.019 0.001 TYR C 154 ARG 0.005 0.001 ARG A 81 ********************** 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 203 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8946 (tp) cc_final: 0.8653 (mt) REVERT: A 195 ASP cc_start: 0.8505 (m-30) cc_final: 0.8253 (m-30) REVERT: A 481 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: B 30 LEU cc_start: 0.8849 (tp) cc_final: 0.8571 (mp) REVERT: B 99 MET cc_start: 0.8162 (ttt) cc_final: 0.7792 (ptm) REVERT: B 185 ARG cc_start: 0.7103 (ttp-110) cc_final: 0.6599 (mtp85) REVERT: B 218 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8525 (m) REVERT: B 429 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7601 (tt) REVERT: B 481 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: C 38 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6611 (tppt) REVERT: C 91 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6459 (t80) REVERT: C 481 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: C 499 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7619 (tp30) outliers start: 44 outliers final: 33 residues processed: 185 average time/residue: 0.2296 time to fit residues: 60.8846 Evaluate side-chains 197 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 100 LEU 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 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 100 LEU Chi-restraints excluded: chain B residue 109 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 319 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 483 VAL 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 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 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 124 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 119 optimal weight: 0.0050 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.151718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110915 restraints weight = 14966.614| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.10 r_work: 0.3146 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11940 Z= 0.176 Angle : 0.543 6.493 16293 Z= 0.281 Chirality : 0.039 0.167 1881 Planarity : 0.004 0.062 1962 Dihedral : 4.348 50.013 1541 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.28 % Allowed : 28.26 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.22), residues: 1476 helix: 2.05 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 182 HIS 0.003 0.001 HIS B 192 PHE 0.038 0.001 PHE B 420 TYR 0.022 0.001 TYR C 154 ARG 0.004 0.000 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2692.03 seconds wall clock time: 49 minutes 47.48 seconds (2987.48 seconds total)