Starting phenix.real_space_refine on Mon Jul 28 13:14:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm2_13510/07_2025/7pm2_13510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm2_13510/07_2025/7pm2_13510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm2_13510/07_2025/7pm2_13510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm2_13510/07_2025/7pm2_13510.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm2_13510/07_2025/7pm2_13510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm2_13510/07_2025/7pm2_13510.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6475 2.51 5 N 1721 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10156 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6117 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 27, 'TRANS': 721} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.28, per 1000 atoms: 0.62 Number of scatterers: 10156 At special positions: 0 Unit cell: (104.5, 133.1, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1893 8.00 N 1721 7.00 C 6475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 56.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.202A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 116 through 120 removed outlier: 4.239A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.755A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.501A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.530A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.595A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.696A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.605A pdb=" N VAL A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.248A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 278 Proline residue: A 272 - end of helix removed outlier: 5.616A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 278 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.160A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.782A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.565A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.652A pdb=" N ASP A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.765A pdb=" N MET A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.632A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.648A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.613A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.522A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.637A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 704 through 712 removed outlier: 4.098A pdb=" N SER A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.698A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.703A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.881A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.627A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.520A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.627A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.696A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.260A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.531A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.439A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 347 removed outlier: 4.473A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 375 removed outlier: 3.922A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.506A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.853A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.655A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.923A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 504 hydrogen bonds defined for protein. 1416 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: 3.16 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2792 1.33 - 1.47: 2913 1.47 - 1.60: 4562 1.60 - 1.73: 3 1.73 - 1.86: 102 Bond restraints: 10372 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" O2 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" O1 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.565 1.509 0.056 2.00e-02 2.50e+03 7.89e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 ... (remaining 10367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 13620 2.21 - 4.42: 340 4.42 - 6.63: 36 6.63 - 8.84: 5 8.84 - 11.05: 7 Bond angle restraints: 14008 Sorted by residual: angle pdb=" CA MET A 783 " pdb=" CB MET A 783 " pdb=" CG MET A 783 " ideal model delta sigma weight residual 114.10 104.80 9.30 2.00e+00 2.50e-01 2.16e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 108.42 103.00 5.42 1.43e+00 4.89e-01 1.44e+01 angle pdb=" C1' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 111.00 99.95 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 128.90 118.29 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C THR A 426 " pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 122.23 127.26 -5.03 1.44e+00 4.82e-01 1.22e+01 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 6128 35.65 - 71.30: 103 71.30 - 106.94: 29 106.94 - 142.59: 6 142.59 - 178.24: 12 Dihedral angle restraints: 6278 sinusoidal: 2599 harmonic: 3679 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 169.96 130.04 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" CA LYS A 584 " pdb=" C LYS A 584 " pdb=" N LYS A 585 " pdb=" CA LYS A 585 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE C 289 " pdb=" C ILE C 289 " pdb=" N ARG C 290 " pdb=" CA ARG C 290 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 6275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1324 0.078 - 0.156: 188 0.156 - 0.234: 11 0.234 - 0.312: 2 0.312 - 0.390: 2 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C10 9UE C 404 " pdb=" C18 9UE C 404 " pdb=" C9 9UE C 404 " pdb=" N2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C3 9UE C 404 " pdb=" O 9UE C 404 " pdb=" C2 9UE C 404 " pdb=" C35 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.21 2.57 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1524 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 701 " 0.160 9.50e-02 1.11e+02 9.19e-02 4.41e+01 pdb=" NE ARG A 701 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 701 " 0.109 2.00e-02 2.50e+03 pdb=" NH1 ARG A 701 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG A 701 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.135 9.50e-02 1.11e+02 7.88e-02 3.39e+01 pdb=" NE ARG A 710 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " -0.096 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " 0.140 9.50e-02 1.11e+02 7.50e-02 2.37e+01 pdb=" NE ARG A 92 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " 0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " -0.021 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 108 2.65 - 3.21: 9680 3.21 - 3.77: 14842 3.77 - 4.34: 20984 4.34 - 4.90: 34216 Nonbonded interactions: 79830 Sorted by model distance: nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 403 " model vdw 2.085 2.170 nonbonded pdb=" OH TYR A 528 " pdb=" O ALA A 547 " model vdw 2.182 3.040 nonbonded pdb=" NH1 ARG A 213 " pdb=" O THR A 443 " model vdw 2.197 3.120 nonbonded pdb=" OG SER A 78 " pdb=" O ALA A 753 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.237 3.040 ... (remaining 79825 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.700 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.004 0.060 10372 Z= 0.211 Angle : 0.859 11.049 14008 Z= 0.497 Chirality : 0.054 0.390 1527 Planarity : 0.008 0.093 1793 Dihedral : 18.701 178.239 3906 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.21), residues: 1238 helix: -1.72 (0.17), residues: 585 sheet: 0.38 (0.38), residues: 157 loop : -0.14 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 356 HIS 0.009 0.002 HIS A 418 PHE 0.020 0.002 PHE A 673 TYR 0.036 0.006 TYR C 198 ARG 0.111 0.011 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.16030 ( 502) hydrogen bonds : angle 7.82157 ( 1416) covalent geometry : bond 0.00448 (10372) covalent geometry : angle 0.85887 (14008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8141 (m-80) cc_final: 0.7475 (m-10) REVERT: B 110 ARG cc_start: 0.8848 (mtt-85) cc_final: 0.8508 (mtt-85) REVERT: B 121 THR cc_start: 0.8417 (p) cc_final: 0.8175 (p) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2757 time to fit residues: 68.1517 Evaluate side-chains 94 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 chunk 112 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 136 ASN A 39 GLN A 264 GLN A 395 HIS ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A 726 GLN C 12 ASN C 59 GLN C 246 GLN C 280 ASN C 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061220 restraints weight = 30776.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.063468 restraints weight = 15048.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.064980 restraints weight = 9408.882| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10372 Z= 0.140 Angle : 0.641 7.781 14008 Z= 0.334 Chirality : 0.044 0.347 1527 Planarity : 0.004 0.036 1793 Dihedral : 18.139 168.293 1427 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.39 % Allowed : 6.09 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1238 helix: 0.66 (0.20), residues: 596 sheet: 0.45 (0.37), residues: 169 loop : 0.54 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 414 HIS 0.010 0.001 HIS A 418 PHE 0.018 0.001 PHE C 255 TYR 0.014 0.001 TYR C 306 ARG 0.007 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 502) hydrogen bonds : angle 5.22198 ( 1416) covalent geometry : bond 0.00309 (10372) covalent geometry : angle 0.64063 (14008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 ILE cc_start: 0.7712 (mt) cc_final: 0.7452 (mp) REVERT: B 110 ARG cc_start: 0.8956 (mtt-85) cc_final: 0.8557 (mtt-85) REVERT: B 120 MET cc_start: 0.7016 (mmm) cc_final: 0.6483 (mmp) REVERT: B 121 THR cc_start: 0.8340 (p) cc_final: 0.8101 (p) REVERT: A 749 ILE cc_start: 0.9259 (tt) cc_final: 0.9027 (tt) REVERT: C 107 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6980 (tm-30) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.2462 time to fit residues: 45.8034 Evaluate side-chains 105 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059726 restraints weight = 31362.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061966 restraints weight = 15255.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063471 restraints weight = 9518.863| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10372 Z= 0.155 Angle : 0.596 10.718 14008 Z= 0.305 Chirality : 0.043 0.270 1527 Planarity : 0.004 0.037 1793 Dihedral : 17.361 169.081 1427 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.57 % Allowed : 8.49 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.23), residues: 1238 helix: 1.36 (0.21), residues: 599 sheet: 0.53 (0.38), residues: 169 loop : 0.61 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.010 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.016 0.001 TYR A 711 ARG 0.005 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 502) hydrogen bonds : angle 4.86457 ( 1416) covalent geometry : bond 0.00351 (10372) covalent geometry : angle 0.59583 (14008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8721 (m-80) cc_final: 0.8494 (m-80) REVERT: B 110 ARG cc_start: 0.8962 (mtt-85) cc_final: 0.8598 (mtt-85) REVERT: A 398 ASN cc_start: 0.9470 (m-40) cc_final: 0.9046 (m-40) REVERT: A 749 ILE cc_start: 0.9272 (tt) cc_final: 0.9055 (tt) REVERT: C 107 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6983 (tm-30) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.2248 time to fit residues: 38.8168 Evaluate side-chains 101 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN C 137 GLN C 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.082514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060192 restraints weight = 31021.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.062459 restraints weight = 14907.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063990 restraints weight = 9313.568| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10372 Z= 0.158 Angle : 0.592 11.678 14008 Z= 0.298 Chirality : 0.043 0.324 1527 Planarity : 0.004 0.038 1793 Dihedral : 16.498 169.164 1427 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.85 % Allowed : 9.51 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1238 helix: 1.53 (0.21), residues: 611 sheet: 0.53 (0.38), residues: 169 loop : 0.65 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.009 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.014 0.001 TYR A 711 ARG 0.004 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 502) hydrogen bonds : angle 4.72133 ( 1416) covalent geometry : bond 0.00361 (10372) covalent geometry : angle 0.59212 (14008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8855 (mp10) cc_final: 0.8556 (mp10) REVERT: B 93 PHE cc_start: 0.8708 (m-80) cc_final: 0.8488 (m-80) REVERT: B 110 ARG cc_start: 0.9007 (mtt-85) cc_final: 0.8641 (mtt-85) REVERT: A 398 ASN cc_start: 0.9464 (m-40) cc_final: 0.9045 (m-40) REVERT: C 107 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: C 371 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7574 (m90) outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.2030 time to fit residues: 34.1663 Evaluate side-chains 107 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 chunk 70 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 775 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.083316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061136 restraints weight = 31017.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063438 restraints weight = 14882.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.064967 restraints weight = 9253.364| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10372 Z= 0.117 Angle : 0.561 13.113 14008 Z= 0.280 Chirality : 0.042 0.328 1527 Planarity : 0.004 0.039 1793 Dihedral : 15.837 170.609 1427 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.94 % Allowed : 9.42 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.24), residues: 1238 helix: 1.69 (0.21), residues: 616 sheet: 0.55 (0.39), residues: 169 loop : 0.74 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.009 0.001 HIS A 418 PHE 0.011 0.001 PHE C 255 TYR 0.014 0.001 TYR A 787 ARG 0.004 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 502) hydrogen bonds : angle 4.54287 ( 1416) covalent geometry : bond 0.00267 (10372) covalent geometry : angle 0.56076 (14008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8453 (tp-100) REVERT: B 31 GLN cc_start: 0.8790 (mp10) cc_final: 0.8353 (mp10) REVERT: B 93 PHE cc_start: 0.8686 (m-80) cc_final: 0.8461 (m-80) REVERT: B 110 ARG cc_start: 0.9000 (mtt-85) cc_final: 0.8605 (mtt-85) REVERT: B 120 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7222 (mpp) REVERT: A 135 MET cc_start: 0.7919 (mmm) cc_final: 0.7632 (mmm) REVERT: A 177 MET cc_start: 0.8431 (ppp) cc_final: 0.8216 (ppp) REVERT: A 398 ASN cc_start: 0.9449 (m-40) cc_final: 0.9080 (m-40) REVERT: A 783 MET cc_start: 0.8092 (tpp) cc_final: 0.7888 (tpp) REVERT: C 107 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: C 289 ILE cc_start: 0.8850 (mp) cc_final: 0.8585 (tt) REVERT: C 371 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7543 (m90) outliers start: 21 outliers final: 16 residues processed: 115 average time/residue: 0.2294 time to fit residues: 38.8303 Evaluate side-chains 112 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 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 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060564 restraints weight = 31408.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062829 restraints weight = 15036.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064369 restraints weight = 9376.763| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10372 Z= 0.129 Angle : 0.549 7.951 14008 Z= 0.276 Chirality : 0.042 0.311 1527 Planarity : 0.004 0.039 1793 Dihedral : 15.806 173.124 1427 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.40 % Allowed : 9.60 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.24), residues: 1238 helix: 1.78 (0.21), residues: 616 sheet: 0.59 (0.39), residues: 167 loop : 0.66 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.024 0.001 PHE B 70 TYR 0.014 0.001 TYR A 787 ARG 0.004 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 502) hydrogen bonds : angle 4.50125 ( 1416) covalent geometry : bond 0.00296 (10372) covalent geometry : angle 0.54878 (14008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8466 (tp40) REVERT: B 31 GLN cc_start: 0.8921 (mp10) cc_final: 0.8493 (mp10) REVERT: B 93 PHE cc_start: 0.8666 (m-80) cc_final: 0.8435 (m-80) REVERT: B 110 ARG cc_start: 0.9026 (mtt-85) cc_final: 0.8650 (mtt-85) REVERT: B 120 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7236 (mpp) REVERT: A 135 MET cc_start: 0.7947 (mmm) cc_final: 0.7598 (mmm) REVERT: A 398 ASN cc_start: 0.9457 (m-40) cc_final: 0.9089 (m-40) REVERT: C 65 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7548 (mt) REVERT: C 227 MET cc_start: 0.9063 (tpp) cc_final: 0.8862 (ttm) REVERT: C 289 ILE cc_start: 0.8862 (mp) cc_final: 0.8629 (tt) REVERT: C 371 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7617 (m90) outliers start: 26 outliers final: 18 residues processed: 115 average time/residue: 0.2180 time to fit residues: 36.4701 Evaluate side-chains 113 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059418 restraints weight = 31613.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061663 restraints weight = 15148.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063171 restraints weight = 9462.425| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10372 Z= 0.168 Angle : 0.564 8.443 14008 Z= 0.288 Chirality : 0.042 0.298 1527 Planarity : 0.004 0.039 1793 Dihedral : 16.175 177.131 1427 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.31 % Allowed : 10.34 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.24), residues: 1238 helix: 1.77 (0.21), residues: 616 sheet: 0.56 (0.40), residues: 167 loop : 0.58 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.013 0.001 PHE A 444 TYR 0.013 0.001 TYR A 711 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 502) hydrogen bonds : angle 4.56768 ( 1416) covalent geometry : bond 0.00386 (10372) covalent geometry : angle 0.56405 (14008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8476 (tp40) REVERT: B 93 PHE cc_start: 0.8674 (m-80) cc_final: 0.8180 (m-80) REVERT: B 110 ARG cc_start: 0.9022 (mtt-85) cc_final: 0.8650 (mtt-85) REVERT: B 120 MET cc_start: 0.7550 (mpp) cc_final: 0.7194 (mpp) REVERT: A 135 MET cc_start: 0.7982 (mmm) cc_final: 0.7589 (mmm) REVERT: A 177 MET cc_start: 0.8365 (ppp) cc_final: 0.8155 (ppp) REVERT: A 671 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7413 (t80) REVERT: C 65 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7571 (mt) REVERT: C 132 MET cc_start: 0.8876 (ptm) cc_final: 0.8636 (ppp) REVERT: C 371 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7537 (m90) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.2463 time to fit residues: 40.5638 Evaluate side-chains 108 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060495 restraints weight = 31189.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062766 restraints weight = 14919.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064282 restraints weight = 9278.441| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10372 Z= 0.126 Angle : 0.552 8.995 14008 Z= 0.281 Chirality : 0.042 0.267 1527 Planarity : 0.004 0.039 1793 Dihedral : 16.287 178.324 1427 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.12 % Allowed : 10.80 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1238 helix: 1.87 (0.21), residues: 605 sheet: 0.63 (0.40), residues: 167 loop : 0.63 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.013 0.001 PHE A 444 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 502) hydrogen bonds : angle 4.53018 ( 1416) covalent geometry : bond 0.00288 (10372) covalent geometry : angle 0.55199 (14008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8450 (tp40) REVERT: B 93 PHE cc_start: 0.8646 (m-80) cc_final: 0.8168 (m-80) REVERT: B 110 ARG cc_start: 0.9032 (mtt-85) cc_final: 0.8655 (mtt-85) REVERT: B 120 MET cc_start: 0.7325 (mpp) cc_final: 0.7066 (mpp) REVERT: A 135 MET cc_start: 0.8039 (mmm) cc_final: 0.7710 (mmm) REVERT: A 177 MET cc_start: 0.8346 (ppp) cc_final: 0.8105 (ppp) REVERT: A 671 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7359 (t80) REVERT: C 65 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7649 (mt) REVERT: C 371 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7592 (m90) outliers start: 23 outliers final: 18 residues processed: 105 average time/residue: 0.2554 time to fit residues: 39.8895 Evaluate side-chains 107 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059286 restraints weight = 31240.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061503 restraints weight = 14956.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062998 restraints weight = 9322.285| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10372 Z= 0.179 Angle : 0.600 15.153 14008 Z= 0.302 Chirality : 0.042 0.251 1527 Planarity : 0.004 0.040 1793 Dihedral : 16.312 178.709 1427 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.03 % Allowed : 10.80 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1238 helix: 1.83 (0.21), residues: 611 sheet: 0.55 (0.40), residues: 169 loop : 0.54 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 PHE 0.013 0.001 PHE A 444 TYR 0.015 0.001 TYR A 711 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 502) hydrogen bonds : angle 4.59187 ( 1416) covalent geometry : bond 0.00409 (10372) covalent geometry : angle 0.60017 (14008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.7894 (t80) cc_final: 0.7657 (t80) REVERT: B 93 PHE cc_start: 0.8676 (m-80) cc_final: 0.8183 (m-80) REVERT: B 110 ARG cc_start: 0.9011 (mtt-85) cc_final: 0.8627 (mtt-85) REVERT: B 120 MET cc_start: 0.7403 (mpp) cc_final: 0.7194 (mpp) REVERT: A 135 MET cc_start: 0.8056 (mmm) cc_final: 0.7699 (mmm) REVERT: A 177 MET cc_start: 0.8363 (ppp) cc_final: 0.8102 (ppp) REVERT: A 671 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7326 (t80) REVERT: A 790 MET cc_start: 0.5111 (ttp) cc_final: 0.4798 (ttp) REVERT: C 65 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7588 (mt) REVERT: C 371 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7528 (m90) outliers start: 22 outliers final: 18 residues processed: 104 average time/residue: 0.2666 time to fit residues: 42.0767 Evaluate side-chains 106 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 113 optimal weight: 0.1980 chunk 47 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.082781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060670 restraints weight = 30669.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062973 restraints weight = 14664.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.064527 restraints weight = 9037.985| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10372 Z= 0.118 Angle : 0.578 12.623 14008 Z= 0.288 Chirality : 0.042 0.233 1527 Planarity : 0.004 0.040 1793 Dihedral : 16.337 178.644 1427 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.03 % Allowed : 10.99 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1238 helix: 1.89 (0.21), residues: 605 sheet: 0.50 (0.40), residues: 168 loop : 0.60 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.006 0.001 HIS C 275 PHE 0.020 0.001 PHE B 12 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 502) hydrogen bonds : angle 4.47219 ( 1416) covalent geometry : bond 0.00267 (10372) covalent geometry : angle 0.57795 (14008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8609 (m-80) cc_final: 0.8198 (m-80) REVERT: B 110 ARG cc_start: 0.9041 (mtt-85) cc_final: 0.8690 (mtt-85) REVERT: A 135 MET cc_start: 0.8097 (mmm) cc_final: 0.7751 (mmm) REVERT: A 177 MET cc_start: 0.8381 (ppp) cc_final: 0.8096 (ppp) REVERT: A 671 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7407 (t80) REVERT: A 790 MET cc_start: 0.5075 (ttp) cc_final: 0.4786 (ttp) REVERT: C 65 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7724 (mt) REVERT: C 107 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: C 371 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7613 (m90) outliers start: 22 outliers final: 16 residues processed: 108 average time/residue: 0.2834 time to fit residues: 45.4982 Evaluate side-chains 104 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 371 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.0670 chunk 93 optimal weight: 0.2980 chunk 79 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 118 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.083494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061622 restraints weight = 30512.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063939 restraints weight = 14525.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065479 restraints weight = 8908.304| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10372 Z= 0.105 Angle : 0.585 12.065 14008 Z= 0.289 Chirality : 0.041 0.222 1527 Planarity : 0.003 0.039 1793 Dihedral : 16.294 178.482 1427 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.94 % Allowed : 11.27 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.73 (0.24), residues: 1238 helix: 1.86 (0.21), residues: 605 sheet: 0.50 (0.40), residues: 168 loop : 0.59 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.026 0.001 PHE B 70 TYR 0.011 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 502) hydrogen bonds : angle 4.49963 ( 1416) covalent geometry : bond 0.00239 (10372) covalent geometry : angle 0.58466 (14008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.31 seconds wall clock time: 72 minutes 32.68 seconds (4352.68 seconds total)