Starting phenix.real_space_refine on Wed Feb 4 12:26:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzw_48770/02_2026/9mzw_48770.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzw_48770/02_2026/9mzw_48770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzw_48770/02_2026/9mzw_48770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzw_48770/02_2026/9mzw_48770.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzw_48770/02_2026/9mzw_48770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzw_48770/02_2026/9mzw_48770.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 61 5.16 5 C 6629 2.51 5 N 1782 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10476 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4521 Classifications: {'peptide': 580} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 553} Chain: "B" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3538 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 1 Chain: "C" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2417 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 286} Chain breaks: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.22 Number of scatterers: 10476 At special positions: 0 Unit cell: (107, 99.51, 121.98, 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 61 16.00 O 2004 8.00 N 1782 7.00 C 6629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 410.5 milliseconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 52.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 43 removed outlier: 3.633A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.888A pdb=" N ASP A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 75 removed outlier: 3.527A pdb=" N GLY A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.768A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.682A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.997A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.529A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.688A pdb=" N ARG A 157 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.543A pdb=" N ARG A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.893A pdb=" N VAL A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 4.265A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.836A pdb=" N GLN A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.652A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.820A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.738A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 317 through 335 removed outlier: 4.397A pdb=" N LEU A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix removed outlier: 3.823A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.680A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 357 through 374 removed outlier: 4.302A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 395 removed outlier: 3.577A pdb=" N ARG A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.296A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 433 removed outlier: 3.527A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix removed outlier: 3.792A pdb=" N GLN A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 4.220A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 3.857A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.108A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.795A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.573A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 567 removed outlier: 4.495A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.770A pdb=" N ALA A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.875A pdb=" N LEU B 225 " --> pdb=" O MET B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 326 through 331 removed outlier: 4.867A pdb=" N SER B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.781A pdb=" N GLU B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.867A pdb=" N LEU B 413 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 18 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.608A pdb=" N GLN C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.761A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.503A pdb=" N ASP C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 removed outlier: 4.000A pdb=" N ARG C 268 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 18 removed outlier: 5.497A pdb=" N PHE B 14 " --> pdb=" O GLN B 443 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN B 443 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 16 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N HIS B 421 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.718A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 52 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR B 76 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 54 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.710A pdb=" N GLU B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 90 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.661A pdb=" N LYS B 98 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 119 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 171 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 121 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS B 129 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP B 161 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.273A pdb=" N LEU B 202 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASN B 213 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS B 204 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER B 211 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA7, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.719A pdb=" N ASP B 290 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 350 removed outlier: 3.610A pdb=" N LEU B 379 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.642A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AB2, first strand: chain 'C' and resid 202 through 203 468 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.95 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: 3473 1.34 - 1.46: 1871 1.46 - 1.58: 5253 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 10686 Sorted by residual: bond pdb=" C LYS A 292 " pdb=" N ASP A 293 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.31e-02 5.83e+03 1.32e+01 bond pdb=" N SER C 24 " pdb=" CA SER C 24 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.58e+00 bond pdb=" N VAL A 507 " pdb=" CA VAL A 507 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.17e-02 7.31e+03 8.48e+00 bond pdb=" N TRP B 203 " pdb=" CA TRP B 203 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.15e-02 7.56e+03 7.33e+00 bond pdb=" N HIS B 204 " pdb=" CA HIS B 204 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.22e-02 6.72e+03 6.89e+00 ... (remaining 10681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14104 1.72 - 3.45: 307 3.45 - 5.17: 54 5.17 - 6.89: 19 6.89 - 8.62: 3 Bond angle restraints: 14487 Sorted by residual: angle pdb=" N GLY C 84 " pdb=" CA GLY C 84 " pdb=" C GLY C 84 " ideal model delta sigma weight residual 112.61 118.24 -5.63 1.60e+00 3.91e-01 1.24e+01 angle pdb=" N THR A 78 " pdb=" CA THR A 78 " pdb=" C THR A 78 " ideal model delta sigma weight residual 113.23 109.07 4.16 1.24e+00 6.50e-01 1.13e+01 angle pdb=" C THR C 147 " pdb=" N ASP C 148 " pdb=" CA ASP C 148 " ideal model delta sigma weight residual 122.06 116.03 6.03 1.86e+00 2.89e-01 1.05e+01 angle pdb=" C ASP C 88 " pdb=" N ARG C 89 " pdb=" CA ARG C 89 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.83e+00 angle pdb=" CA THR C 304 " pdb=" CB THR C 304 " pdb=" OG1 THR C 304 " ideal model delta sigma weight residual 109.60 104.98 4.62 1.50e+00 4.44e-01 9.48e+00 ... (remaining 14482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5634 17.88 - 35.75: 656 35.75 - 53.63: 169 53.63 - 71.51: 24 71.51 - 89.39: 17 Dihedral angle restraints: 6500 sinusoidal: 2636 harmonic: 3864 Sorted by residual: dihedral pdb=" CA ARG C 89 " pdb=" C ARG C 89 " pdb=" N GLY C 90 " pdb=" CA GLY C 90 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA SER B 89 " pdb=" C SER B 89 " pdb=" N LEU B 90 " pdb=" CA LEU B 90 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP C 148 " pdb=" C ASP C 148 " pdb=" N LEU C 149 " pdb=" CA LEU C 149 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1340 0.054 - 0.109: 260 0.109 - 0.163: 33 0.163 - 0.217: 4 0.217 - 0.272: 3 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB ILE A 516 " pdb=" CA ILE A 516 " pdb=" CG1 ILE A 516 " pdb=" CG2 ILE A 516 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASP C 290 " pdb=" N ASP C 290 " pdb=" C ASP C 290 " pdb=" CB ASP C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CG LEU C 166 " pdb=" CB LEU C 166 " pdb=" CD1 LEU C 166 " pdb=" CD2 LEU C 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1637 not shown) Planarity restraints: 1875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 89 " 0.353 9.50e-02 1.11e+02 1.58e-01 1.54e+01 pdb=" NE ARG C 89 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 89 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 89 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 89 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 145 " 0.014 2.00e-02 2.50e+03 1.76e-02 6.17e+00 pdb=" CG TYR C 145 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR C 145 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 145 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 145 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 145 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 145 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 145 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 45 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL C 45 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL C 45 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN C 46 " 0.012 2.00e-02 2.50e+03 ... (remaining 1872 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 6 2.18 - 2.86: 3743 2.86 - 3.54: 14645 3.54 - 4.22: 24684 4.22 - 4.90: 44411 Nonbonded interactions: 87489 Sorted by model distance: nonbonded pdb=" CE1 HIS B 326 " pdb=" OG SER B 361 " model vdw 1.504 3.260 nonbonded pdb=" NE2 HIS B 326 " pdb=" OG SER B 361 " model vdw 1.506 3.120 nonbonded pdb=" NE2 HIS B 326 " pdb=" CB SER B 361 " model vdw 1.654 3.520 nonbonded pdb=" OG1 THR C 304 " pdb=" O PHE C 308 " model vdw 2.113 3.040 nonbonded pdb=" O VAL C 94 " pdb=" OG1 THR C 98 " model vdw 2.147 3.040 ... (remaining 87484 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=0.00 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: 0.640 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.048 10687 Z= 0.199 Angle : 0.651 8.617 14487 Z= 0.361 Chirality : 0.045 0.272 1640 Planarity : 0.005 0.158 1875 Dihedral : 16.664 89.385 3984 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 23.29 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1301 helix: 0.45 (0.23), residues: 560 sheet: -1.53 (0.37), residues: 194 loop : -1.25 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 51 TYR 0.043 0.002 TYR C 145 PHE 0.029 0.002 PHE C 164 TRP 0.016 0.001 TRP B 203 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00387 (10686) covalent geometry : angle 0.65093 (14487) hydrogen bonds : bond 0.17773 ( 468) hydrogen bonds : angle 6.89165 ( 1335) Misc. bond : bond 0.04228 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 CYS cc_start: 0.8233 (t) cc_final: 0.7526 (t) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1008 time to fit residues: 27.3539 Evaluate side-chains 129 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 324 GLN B 363 ASN C 63 HIS ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090419 restraints weight = 19370.172| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.37 r_work: 0.3233 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10687 Z= 0.126 Angle : 0.587 7.962 14487 Z= 0.309 Chirality : 0.043 0.173 1640 Planarity : 0.004 0.062 1875 Dihedral : 4.627 64.434 1421 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.99 % Allowed : 21.08 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1301 helix: 0.64 (0.23), residues: 567 sheet: -1.12 (0.39), residues: 183 loop : -1.16 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.031 0.002 TYR C 145 PHE 0.021 0.001 PHE A 538 TRP 0.013 0.001 TRP B 311 HIS 0.008 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00281 (10686) covalent geometry : angle 0.58688 (14487) hydrogen bonds : bond 0.03888 ( 468) hydrogen bonds : angle 5.30455 ( 1335) Misc. bond : bond 0.00439 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8768 (m) REVERT: A 106 ASP cc_start: 0.8346 (m-30) cc_final: 0.7949 (m-30) REVERT: A 426 TYR cc_start: 0.9013 (t80) cc_final: 0.8530 (t80) REVERT: A 528 MET cc_start: 0.8943 (mtm) cc_final: 0.8713 (mtp) REVERT: B 11 GLN cc_start: 0.8093 (mm110) cc_final: 0.7869 (mm-40) REVERT: B 83 GLU cc_start: 0.8482 (tp30) cc_final: 0.8252 (tp30) REVERT: B 163 MET cc_start: 0.8195 (ttp) cc_final: 0.7944 (ptm) REVERT: B 257 ARG cc_start: 0.7437 (mtp85) cc_final: 0.6820 (mtm180) REVERT: B 341 CYS cc_start: 0.8555 (t) cc_final: 0.7600 (t) REVERT: B 380 GLU cc_start: 0.8609 (tt0) cc_final: 0.8109 (tm-30) REVERT: C 66 MET cc_start: 0.8846 (mmm) cc_final: 0.8603 (mmm) REVERT: C 127 TYR cc_start: 0.7545 (m-80) cc_final: 0.7111 (m-10) outliers start: 35 outliers final: 11 residues processed: 165 average time/residue: 0.0767 time to fit residues: 19.3125 Evaluate side-chains 127 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 211 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.119006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091097 restraints weight = 19159.863| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.12 r_work: 0.3239 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10687 Z= 0.125 Angle : 0.552 7.446 14487 Z= 0.290 Chirality : 0.042 0.154 1640 Planarity : 0.004 0.047 1875 Dihedral : 4.526 61.697 1421 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.07 % Allowed : 20.56 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1301 helix: 0.89 (0.23), residues: 570 sheet: -0.79 (0.40), residues: 179 loop : -1.04 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.032 0.002 TYR C 145 PHE 0.020 0.001 PHE A 538 TRP 0.011 0.001 TRP B 203 HIS 0.011 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00285 (10686) covalent geometry : angle 0.55205 (14487) hydrogen bonds : bond 0.03500 ( 468) hydrogen bonds : angle 4.97186 ( 1335) Misc. bond : bond 0.00254 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8251 (mm-30) REVERT: A 21 ARG cc_start: 0.8707 (ttt180) cc_final: 0.8363 (ttt-90) REVERT: A 76 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7818 (t80) REVERT: A 103 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8839 (m) REVERT: A 106 ASP cc_start: 0.8335 (m-30) cc_final: 0.8016 (m-30) REVERT: A 426 TYR cc_start: 0.9139 (t80) cc_final: 0.8499 (t80) REVERT: A 440 ASP cc_start: 0.8332 (m-30) cc_final: 0.8123 (m-30) REVERT: B 83 GLU cc_start: 0.8488 (tp30) cc_final: 0.8221 (tp30) REVERT: B 163 MET cc_start: 0.8268 (ttp) cc_final: 0.7965 (ptm) REVERT: B 257 ARG cc_start: 0.7549 (mtp85) cc_final: 0.6797 (mtm180) REVERT: B 290 ASP cc_start: 0.8246 (p0) cc_final: 0.7646 (p0) REVERT: B 341 CYS cc_start: 0.8605 (t) cc_final: 0.7659 (t) REVERT: C 66 MET cc_start: 0.8880 (mmm) cc_final: 0.8641 (mmm) REVERT: C 197 ASP cc_start: 0.8220 (m-30) cc_final: 0.7714 (m-30) REVERT: C 201 SER cc_start: 0.8761 (m) cc_final: 0.8471 (m) outliers start: 36 outliers final: 19 residues processed: 153 average time/residue: 0.0745 time to fit residues: 17.7569 Evaluate side-chains 140 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 284 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 0.0050 chunk 88 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.120870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091228 restraints weight = 19632.120| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.37 r_work: 0.3244 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10687 Z= 0.107 Angle : 0.526 7.264 14487 Z= 0.276 Chirality : 0.042 0.148 1640 Planarity : 0.004 0.040 1875 Dihedral : 4.421 57.429 1421 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.47 % Allowed : 21.16 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1301 helix: 1.01 (0.23), residues: 575 sheet: -0.58 (0.41), residues: 179 loop : -0.89 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 527 TYR 0.027 0.002 TYR A 495 PHE 0.020 0.001 PHE B 14 TRP 0.012 0.001 TRP B 203 HIS 0.010 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00240 (10686) covalent geometry : angle 0.52566 (14487) hydrogen bonds : bond 0.03168 ( 468) hydrogen bonds : angle 4.75859 ( 1335) Misc. bond : bond 0.00426 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: A 76 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7799 (t80) REVERT: A 103 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8821 (m) REVERT: A 106 ASP cc_start: 0.8371 (m-30) cc_final: 0.8047 (m-30) REVERT: A 250 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8431 (mp10) REVERT: A 426 TYR cc_start: 0.9156 (t80) cc_final: 0.8384 (t80) REVERT: A 440 ASP cc_start: 0.8359 (m-30) cc_final: 0.8095 (m-30) REVERT: B 83 GLU cc_start: 0.8519 (tp30) cc_final: 0.8224 (tp30) REVERT: B 257 ARG cc_start: 0.7537 (mtp85) cc_final: 0.6785 (mtm180) REVERT: B 341 CYS cc_start: 0.8609 (t) cc_final: 0.7702 (t) REVERT: B 380 GLU cc_start: 0.8568 (tt0) cc_final: 0.7478 (pp20) REVERT: C 66 MET cc_start: 0.8874 (mmm) cc_final: 0.8632 (mmm) REVERT: C 80 TYR cc_start: 0.9015 (m-80) cc_final: 0.8598 (m-80) REVERT: C 197 ASP cc_start: 0.8230 (m-30) cc_final: 0.7782 (m-30) REVERT: C 201 SER cc_start: 0.8894 (m) cc_final: 0.8689 (m) outliers start: 29 outliers final: 17 residues processed: 156 average time/residue: 0.0790 time to fit residues: 19.1447 Evaluate side-chains 143 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091266 restraints weight = 19691.068| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.36 r_work: 0.3245 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10687 Z= 0.116 Angle : 0.537 7.680 14487 Z= 0.278 Chirality : 0.042 0.150 1640 Planarity : 0.004 0.043 1875 Dihedral : 4.352 51.825 1421 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.73 % Allowed : 21.25 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1301 helix: 1.10 (0.23), residues: 574 sheet: -0.57 (0.40), residues: 184 loop : -0.82 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 527 TYR 0.025 0.002 TYR A 495 PHE 0.017 0.001 PHE A 538 TRP 0.012 0.001 TRP B 203 HIS 0.009 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00266 (10686) covalent geometry : angle 0.53741 (14487) hydrogen bonds : bond 0.03145 ( 468) hydrogen bonds : angle 4.69453 ( 1335) Misc. bond : bond 0.00335 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: A 76 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7779 (t80) REVERT: A 103 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8826 (m) REVERT: A 106 ASP cc_start: 0.8374 (m-30) cc_final: 0.8054 (m-30) REVERT: A 426 TYR cc_start: 0.9163 (t80) cc_final: 0.8321 (t80) REVERT: A 440 ASP cc_start: 0.8403 (m-30) cc_final: 0.8147 (m-30) REVERT: B 31 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8984 (mp) REVERT: B 83 GLU cc_start: 0.8490 (tp30) cc_final: 0.8276 (tp30) REVERT: B 257 ARG cc_start: 0.7553 (mtp85) cc_final: 0.6833 (mtm180) REVERT: B 324 GLN cc_start: 0.9103 (mm110) cc_final: 0.8880 (mm-40) REVERT: B 333 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.8893 (pt) REVERT: B 341 CYS cc_start: 0.8618 (t) cc_final: 0.7779 (t) REVERT: C 66 MET cc_start: 0.8918 (mmm) cc_final: 0.8681 (mmm) REVERT: C 80 TYR cc_start: 0.9033 (m-80) cc_final: 0.8697 (m-80) REVERT: C 197 ASP cc_start: 0.8246 (m-30) cc_final: 0.7805 (m-30) REVERT: C 201 SER cc_start: 0.8890 (m) cc_final: 0.8651 (m) outliers start: 32 outliers final: 20 residues processed: 154 average time/residue: 0.0684 time to fit residues: 16.8248 Evaluate side-chains 146 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.113706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085486 restraints weight = 19473.792| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.14 r_work: 0.3145 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 10687 Z= 0.292 Angle : 0.627 7.479 14487 Z= 0.329 Chirality : 0.046 0.168 1640 Planarity : 0.004 0.067 1875 Dihedral : 4.705 52.432 1421 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.82 % Allowed : 22.61 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1301 helix: 0.98 (0.23), residues: 574 sheet: -0.90 (0.38), residues: 195 loop : -0.81 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 239 TYR 0.035 0.002 TYR A 495 PHE 0.029 0.002 PHE A 538 TRP 0.016 0.001 TRP B 203 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00684 (10686) covalent geometry : angle 0.62675 (14487) hydrogen bonds : bond 0.04088 ( 468) hydrogen bonds : angle 5.08998 ( 1335) Misc. bond : bond 0.00457 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8298 (mm-30) REVERT: A 106 ASP cc_start: 0.8335 (m-30) cc_final: 0.7940 (m-30) REVERT: B 83 GLU cc_start: 0.8552 (tp30) cc_final: 0.8285 (tp30) REVERT: B 221 ASN cc_start: 0.9305 (t0) cc_final: 0.9060 (t0) REVERT: B 341 CYS cc_start: 0.8670 (t) cc_final: 0.7888 (t) REVERT: C 66 MET cc_start: 0.8932 (mmm) cc_final: 0.8689 (mmm) REVERT: C 197 ASP cc_start: 0.8265 (m-30) cc_final: 0.7867 (m-30) outliers start: 33 outliers final: 24 residues processed: 139 average time/residue: 0.0738 time to fit residues: 16.0581 Evaluate side-chains 130 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 284 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 127 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086981 restraints weight = 19070.856| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.08 r_work: 0.3179 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10687 Z= 0.195 Angle : 0.575 7.117 14487 Z= 0.302 Chirality : 0.044 0.179 1640 Planarity : 0.004 0.049 1875 Dihedral : 4.642 50.171 1421 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.82 % Allowed : 23.29 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.24), residues: 1301 helix: 1.06 (0.23), residues: 572 sheet: -0.77 (0.40), residues: 177 loop : -0.79 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 106 TYR 0.029 0.002 TYR A 495 PHE 0.023 0.001 PHE A 538 TRP 0.013 0.001 TRP B 203 HIS 0.004 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00461 (10686) covalent geometry : angle 0.57479 (14487) hydrogen bonds : bond 0.03642 ( 468) hydrogen bonds : angle 4.96590 ( 1335) Misc. bond : bond 0.00671 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: A 103 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8858 (m) REVERT: A 106 ASP cc_start: 0.8327 (m-30) cc_final: 0.7947 (m-30) REVERT: B 83 GLU cc_start: 0.8531 (tp30) cc_final: 0.8279 (tp30) REVERT: B 257 ARG cc_start: 0.7416 (mtp85) cc_final: 0.6874 (mtm180) REVERT: B 333 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.8885 (pt) REVERT: B 341 CYS cc_start: 0.8656 (t) cc_final: 0.7933 (t) REVERT: B 445 LYS cc_start: 0.6942 (tttt) cc_final: 0.6647 (mttt) REVERT: C 66 MET cc_start: 0.8939 (mmm) cc_final: 0.8722 (mmm) REVERT: C 132 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7989 (tm-30) outliers start: 33 outliers final: 27 residues processed: 149 average time/residue: 0.0751 time to fit residues: 17.3394 Evaluate side-chains 143 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 284 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 0.0040 chunk 32 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.116537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086138 restraints weight = 19487.358| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.36 r_work: 0.3208 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10687 Z= 0.170 Angle : 0.571 8.511 14487 Z= 0.298 Chirality : 0.043 0.212 1640 Planarity : 0.004 0.070 1875 Dihedral : 4.613 46.895 1421 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.73 % Allowed : 23.04 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1301 helix: 1.07 (0.23), residues: 575 sheet: -0.70 (0.40), residues: 176 loop : -0.73 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 106 TYR 0.025 0.002 TYR A 495 PHE 0.022 0.001 PHE B 14 TRP 0.017 0.001 TRP B 203 HIS 0.004 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00403 (10686) covalent geometry : angle 0.57104 (14487) hydrogen bonds : bond 0.03528 ( 468) hydrogen bonds : angle 4.91734 ( 1335) Misc. bond : bond 0.01105 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: A 103 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8826 (m) REVERT: A 106 ASP cc_start: 0.8337 (m-30) cc_final: 0.7959 (m-30) REVERT: A 250 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: B 83 GLU cc_start: 0.8477 (tp30) cc_final: 0.8229 (tp30) REVERT: B 257 ARG cc_start: 0.7335 (mtp85) cc_final: 0.6856 (mtm180) REVERT: B 333 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.8878 (pt) REVERT: B 341 CYS cc_start: 0.8691 (t) cc_final: 0.8067 (t) REVERT: C 66 MET cc_start: 0.8879 (mmm) cc_final: 0.8662 (mmm) REVERT: C 132 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7923 (tm-30) outliers start: 32 outliers final: 27 residues processed: 145 average time/residue: 0.0830 time to fit residues: 18.6744 Evaluate side-chains 146 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 284 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.115763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087901 restraints weight = 19144.721| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.08 r_work: 0.3196 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 10687 Z= 0.168 Angle : 0.570 7.781 14487 Z= 0.297 Chirality : 0.044 0.214 1640 Planarity : 0.004 0.062 1875 Dihedral : 4.561 42.094 1421 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.90 % Allowed : 23.12 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1301 helix: 1.11 (0.23), residues: 574 sheet: -0.69 (0.40), residues: 176 loop : -0.73 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 106 TYR 0.025 0.002 TYR A 495 PHE 0.029 0.001 PHE C 164 TRP 0.022 0.001 TRP B 203 HIS 0.004 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00400 (10686) covalent geometry : angle 0.57049 (14487) hydrogen bonds : bond 0.03454 ( 468) hydrogen bonds : angle 4.90625 ( 1335) Misc. bond : bond 0.01052 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8250 (mm-30) REVERT: A 106 ASP cc_start: 0.8346 (m-30) cc_final: 0.7967 (m-30) REVERT: A 250 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8525 (mp10) REVERT: A 350 MET cc_start: 0.8890 (mmt) cc_final: 0.8343 (mmt) REVERT: A 581 GLU cc_start: 0.8632 (tt0) cc_final: 0.8370 (tt0) REVERT: B 83 GLU cc_start: 0.8520 (tp30) cc_final: 0.8279 (tp30) REVERT: B 257 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6893 (mtm180) REVERT: B 333 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.8831 (pt) REVERT: B 341 CYS cc_start: 0.8671 (t) cc_final: 0.8018 (t) REVERT: C 66 MET cc_start: 0.8887 (mmm) cc_final: 0.8670 (mmm) REVERT: C 132 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7923 (tm-30) outliers start: 34 outliers final: 27 residues processed: 150 average time/residue: 0.0871 time to fit residues: 19.8994 Evaluate side-chains 148 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.118389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089542 restraints weight = 19530.366| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.30 r_work: 0.3217 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10687 Z= 0.126 Angle : 0.561 13.113 14487 Z= 0.288 Chirality : 0.042 0.179 1640 Planarity : 0.004 0.054 1875 Dihedral : 4.443 36.680 1421 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.47 % Allowed : 23.29 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1301 helix: 1.16 (0.23), residues: 576 sheet: -0.65 (0.40), residues: 177 loop : -0.72 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.022 0.001 TYR A 495 PHE 0.024 0.001 PHE B 14 TRP 0.021 0.001 TRP B 203 HIS 0.003 0.001 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.00297 (10686) covalent geometry : angle 0.56129 (14487) hydrogen bonds : bond 0.03200 ( 468) hydrogen bonds : angle 4.80562 ( 1335) Misc. bond : bond 0.00873 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8281 (mm-30) REVERT: A 106 ASP cc_start: 0.8421 (m-30) cc_final: 0.8128 (m-30) REVERT: A 250 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8496 (mp10) REVERT: A 350 MET cc_start: 0.8808 (mmt) cc_final: 0.8375 (mmt) REVERT: A 508 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 581 GLU cc_start: 0.8716 (tt0) cc_final: 0.8443 (tt0) REVERT: B 83 GLU cc_start: 0.8485 (tp30) cc_final: 0.8246 (tp30) REVERT: B 257 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6876 (mtm180) REVERT: B 290 ASP cc_start: 0.7964 (p0) cc_final: 0.7506 (p0) REVERT: B 324 GLN cc_start: 0.9045 (mm110) cc_final: 0.8778 (mm-40) REVERT: B 333 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.8746 (pt) REVERT: B 341 CYS cc_start: 0.8507 (t) cc_final: 0.7867 (t) REVERT: C 66 MET cc_start: 0.8860 (mmm) cc_final: 0.8637 (mmm) REVERT: C 132 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7891 (tm-30) outliers start: 29 outliers final: 24 residues processed: 149 average time/residue: 0.0861 time to fit residues: 19.6681 Evaluate side-chains 149 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 38 optimal weight: 0.0470 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.118324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089304 restraints weight = 19769.471| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.31 r_work: 0.3214 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10687 Z= 0.133 Angle : 0.567 12.046 14487 Z= 0.290 Chirality : 0.043 0.168 1640 Planarity : 0.004 0.052 1875 Dihedral : 4.401 32.867 1421 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 23.89 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1301 helix: 1.21 (0.23), residues: 577 sheet: -0.61 (0.40), residues: 177 loop : -0.71 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 527 TYR 0.027 0.002 TYR A 577 PHE 0.027 0.001 PHE C 164 TRP 0.019 0.001 TRP B 203 HIS 0.005 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00313 (10686) covalent geometry : angle 0.56723 (14487) hydrogen bonds : bond 0.03194 ( 468) hydrogen bonds : angle 4.78406 ( 1335) Misc. bond : bond 0.00864 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2343.40 seconds wall clock time: 41 minutes 2.22 seconds (2462.22 seconds total)