Starting phenix.real_space_refine on Tue Jul 29 04:07:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrm_14919/07_2025/7zrm_14919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrm_14919/07_2025/7zrm_14919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2025/7zrm_14919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2025/7zrm_14919.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2025/7zrm_14919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrm_14919/07_2025/7zrm_14919.cif" } resolution = 3.7 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= 0.007 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 K 5 8.98 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6971 2.51 5 N 1826 2.21 5 O 1971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10839 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5020 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.44, per 1000 atoms: 0.69 Number of scatterers: 10839 At special positions: 0 Unit cell: (94.116, 110.308, 149.776, 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) K 5 19.00 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1971 8.00 N 1826 7.00 C 6971 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 62.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix removed outlier: 3.986A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 133 through 157 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 4.122A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.883A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.528A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 305 removed outlier: 4.067A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.965A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.588A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.059A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 Proline residue: A 499 - end of helix removed outlier: 3.795A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 550 removed outlier: 4.019A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 3 through 21 removed outlier: 3.804A pdb=" N ALA C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.833A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 25 removed outlier: 4.590A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 32 removed outlier: 4.497A pdb=" N ARG B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 55 removed outlier: 3.522A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 97 removed outlier: 3.832A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 4.124A pdb=" N GLN B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 207 removed outlier: 4.099A pdb=" N VAL B 207 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 247 removed outlier: 3.844A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.569A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 285 removed outlier: 5.823A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.980A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 removed outlier: 3.843A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 452 through 464 Processing helix chain 'B' and resid 474 through 484 removed outlier: 3.801A pdb=" N GLU B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 4.141A pdb=" N LYS B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 557 through 595 removed outlier: 4.097A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 3.809A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.838A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 removed outlier: 3.868A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 658 Processing helix chain 'B' and resid 658 through 680 Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.915A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.718A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 107 removed outlier: 3.553A pdb=" N ALA B 106 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.542A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA8, first strand: chain 'B' and resid 165 through 168 removed outlier: 3.849A pdb=" N VAL B 165 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.199A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 517 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 removed outlier: 7.573A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 319 through 322 removed outlier: 7.573A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1929 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: 4.11 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1767 1.32 - 1.44: 2731 1.44 - 1.57: 6421 1.57 - 1.70: 4 1.70 - 1.82: 112 Bond restraints: 11035 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.593 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C ASN B 26 " pdb=" N PRO B 27 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.57e+00 bond pdb=" CG PHD B 307 " pdb=" OD1 PHD B 307 " ideal model delta sigma weight residual 1.300 1.330 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" SD MET A 489 " pdb=" CE MET A 489 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.17e+00 bond pdb=" CB PRO B 164 " pdb=" CG PRO B 164 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.93e+00 ... (remaining 11030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 14697 2.33 - 4.66: 246 4.66 - 6.99: 66 6.99 - 9.32: 14 9.32 - 11.65: 3 Bond angle restraints: 15026 Sorted by residual: angle pdb=" C GLY A 374 " pdb=" N GLY A 375 " pdb=" CA GLY A 375 " ideal model delta sigma weight residual 121.41 130.73 -9.32 1.96e+00 2.60e-01 2.26e+01 angle pdb=" CB MET A 501 " pdb=" CG MET A 501 " pdb=" SD MET A 501 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C PHE A 471 " pdb=" N ALA A 472 " pdb=" CA ALA A 472 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.47 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO B 27 " pdb=" N GLN B 28 " pdb=" CA GLN B 28 " ideal model delta sigma weight residual 122.08 127.12 -5.04 1.47e+00 4.63e-01 1.17e+01 ... (remaining 15021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 6172 24.60 - 49.19: 345 49.19 - 73.79: 29 73.79 - 98.38: 8 98.38 - 122.98: 1 Dihedral angle restraints: 6555 sinusoidal: 2449 harmonic: 4106 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 62.97 -122.98 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" CA THR A 542 " pdb=" C THR A 542 " pdb=" N PHE A 543 " pdb=" CA PHE A 543 " ideal model delta harmonic sigma weight residual 180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA GLY A 495 " pdb=" C GLY A 495 " pdb=" N VAL A 496 " pdb=" CA VAL A 496 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1361 0.051 - 0.101: 365 0.101 - 0.152: 75 0.152 - 0.203: 8 0.203 - 0.253: 2 Chirality restraints: 1811 Sorted by residual: chirality pdb=" CB ILE A 348 " pdb=" CA ILE A 348 " pdb=" CG1 ILE A 348 " pdb=" CG2 ILE A 348 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU A 77 " pdb=" CB LEU A 77 " pdb=" CD1 LEU A 77 " pdb=" CD2 LEU A 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1808 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 163 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 164 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 100 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C VAL B 100 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL B 100 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 101 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO B 496 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.035 5.00e-02 4.00e+02 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 3415 2.84 - 3.41: 12354 3.41 - 3.99: 20829 3.99 - 4.56: 29249 4.56 - 5.14: 42180 Nonbonded interactions: 108027 Sorted by model distance: nonbonded pdb=" O GLU A 413 " pdb=" OG1 THR A 417 " model vdw 2.260 3.040 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.265 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.265 3.040 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OD1 ASN A 466 " model vdw 2.305 3.040 ... (remaining 108022 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: 2.950 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.420 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 0.223 11035 Z= 0.209 Angle : 0.808 11.653 15026 Z= 0.402 Chirality : 0.048 0.253 1811 Planarity : 0.006 0.101 1902 Dihedral : 14.868 122.976 3917 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.35 (0.20), residues: 1439 helix: 0.02 (0.16), residues: 864 sheet: -1.95 (0.59), residues: 74 loop : -2.29 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 176 HIS 0.005 0.001 HIS A 242 PHE 0.023 0.002 PHE A 109 TYR 0.034 0.002 TYR A 381 ARG 0.013 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.10641 ( 653) hydrogen bonds : angle 5.32308 ( 1929) covalent geometry : bond 0.00437 (11035) covalent geometry : angle 0.80839 (15026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.276 Fit side-chains REVERT: A 360 MET cc_start: 0.7207 (tmm) cc_final: 0.6960 (tmm) REVERT: C 170 TYR cc_start: 0.6769 (p90) cc_final: 0.6355 (p90) REVERT: D 21 TYR cc_start: 0.7067 (t80) cc_final: 0.6453 (t80) REVERT: B 36 MET cc_start: 0.7431 (mmt) cc_final: 0.7136 (mmt) REVERT: B 74 ILE cc_start: 0.7513 (pt) cc_final: 0.7143 (mt) REVERT: B 101 LYS cc_start: 0.6504 (mtmm) cc_final: 0.6014 (pptt) REVERT: B 332 THR cc_start: 0.6743 (p) cc_final: 0.6405 (t) REVERT: B 383 MET cc_start: 0.5847 (ppp) cc_final: 0.5314 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1972 time to fit residues: 53.7611 Evaluate side-chains 150 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 129 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN B 217 ASN B 459 GLN B 521 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118231 restraints weight = 16826.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120363 restraints weight = 9074.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121653 restraints weight = 6079.906| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11035 Z= 0.119 Angle : 0.552 6.359 15026 Z= 0.275 Chirality : 0.039 0.148 1811 Planarity : 0.005 0.053 1902 Dihedral : 5.849 119.166 1537 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.71 % Allowed : 8.64 % Favored : 90.65 % 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: -0.39 (0.22), residues: 1439 helix: 0.89 (0.17), residues: 864 sheet: -1.16 (0.75), residues: 50 loop : -2.15 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 176 HIS 0.002 0.001 HIS A 451 PHE 0.012 0.001 PHE A 373 TYR 0.028 0.001 TYR A 381 ARG 0.004 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 653) hydrogen bonds : angle 4.43782 ( 1929) covalent geometry : bond 0.00257 (11035) covalent geometry : angle 0.55209 (15026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 1.176 Fit side-chains REVERT: A 360 MET cc_start: 0.7284 (tmm) cc_final: 0.7052 (tmm) REVERT: A 367 GLN cc_start: 0.7982 (mt0) cc_final: 0.7674 (mt0) REVERT: C 170 TYR cc_start: 0.6750 (p90) cc_final: 0.6447 (p90) REVERT: B 101 LYS cc_start: 0.6524 (mtmm) cc_final: 0.5997 (pptt) REVERT: B 203 MET cc_start: 0.6545 (ptt) cc_final: 0.6342 (ptt) REVERT: B 332 THR cc_start: 0.6816 (p) cc_final: 0.6474 (t) REVERT: B 383 MET cc_start: 0.5942 (ppp) cc_final: 0.5445 (tpp) outliers start: 8 outliers final: 6 residues processed: 165 average time/residue: 0.2589 time to fit residues: 64.5852 Evaluate side-chains 150 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 111 optimal weight: 0.0980 chunk 119 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 319 ASN A 466 ASN B 563 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.146146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117883 restraints weight = 17199.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120021 restraints weight = 9279.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121131 restraints weight = 6221.000| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11035 Z= 0.109 Angle : 0.525 6.639 15026 Z= 0.261 Chirality : 0.039 0.149 1811 Planarity : 0.004 0.051 1902 Dihedral : 5.721 117.285 1537 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.06 % Allowed : 11.38 % Favored : 87.57 % 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: -0.03 (0.22), residues: 1439 helix: 1.32 (0.18), residues: 845 sheet: -1.23 (0.76), residues: 50 loop : -2.15 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 176 HIS 0.002 0.001 HIS A 242 PHE 0.012 0.001 PHE A 494 TYR 0.025 0.001 TYR A 381 ARG 0.004 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 653) hydrogen bonds : angle 4.26772 ( 1929) covalent geometry : bond 0.00235 (11035) covalent geometry : angle 0.52470 (15026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.102 Fit side-chains REVERT: A 366 MET cc_start: 0.8642 (ttm) cc_final: 0.8304 (ttm) REVERT: A 367 GLN cc_start: 0.8112 (mt0) cc_final: 0.7864 (mt0) REVERT: C 170 TYR cc_start: 0.6816 (p90) cc_final: 0.6492 (p90) REVERT: B 101 LYS cc_start: 0.6607 (mtmm) cc_final: 0.6065 (pptt) REVERT: B 131 ILE cc_start: 0.6810 (tp) cc_final: 0.6557 (tt) REVERT: B 306 LEU cc_start: 0.8794 (mt) cc_final: 0.8476 (mt) REVERT: B 383 MET cc_start: 0.6190 (ppp) cc_final: 0.5706 (tpp) outliers start: 12 outliers final: 9 residues processed: 158 average time/residue: 0.1956 time to fit residues: 47.2284 Evaluate side-chains 157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 137 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 129 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.143983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115254 restraints weight = 17031.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117353 restraints weight = 9302.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118677 restraints weight = 6295.320| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11035 Z= 0.132 Angle : 0.534 6.282 15026 Z= 0.267 Chirality : 0.039 0.152 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.666 116.175 1537 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.94 % Allowed : 13.32 % Favored : 84.74 % 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: 0.10 (0.22), residues: 1439 helix: 1.45 (0.18), residues: 846 sheet: -1.31 (0.75), residues: 50 loop : -2.12 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 176 HIS 0.002 0.001 HIS A 351 PHE 0.013 0.001 PHE A 494 TYR 0.023 0.001 TYR A 381 ARG 0.004 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 653) hydrogen bonds : angle 4.25019 ( 1929) covalent geometry : bond 0.00298 (11035) covalent geometry : angle 0.53410 (15026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.244 Fit side-chains REVERT: A 366 MET cc_start: 0.8789 (ttm) cc_final: 0.8493 (ttm) REVERT: A 367 GLN cc_start: 0.8240 (mt0) cc_final: 0.7956 (mt0) REVERT: B 36 MET cc_start: 0.7337 (mmt) cc_final: 0.7078 (mmt) REVERT: B 101 LYS cc_start: 0.6668 (mtmm) cc_final: 0.6076 (pptt) REVERT: B 131 ILE cc_start: 0.6906 (tp) cc_final: 0.6610 (tt) REVERT: B 186 TRP cc_start: 0.2603 (p-90) cc_final: 0.2393 (p-90) REVERT: B 383 MET cc_start: 0.6221 (ppp) cc_final: 0.5857 (tpp) REVERT: B 465 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7767 (mp) outliers start: 22 outliers final: 13 residues processed: 165 average time/residue: 0.2521 time to fit residues: 61.7464 Evaluate side-chains 160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 127 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 9 optimal weight: 0.0470 chunk 122 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 131 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** D 25 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.144557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117282 restraints weight = 17035.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117817 restraints weight = 9508.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118757 restraints weight = 6912.389| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11035 Z= 0.112 Angle : 0.523 8.144 15026 Z= 0.260 Chirality : 0.039 0.147 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.519 114.923 1537 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.41 % Allowed : 15.87 % Favored : 82.72 % 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: 0.21 (0.22), residues: 1439 helix: 1.50 (0.18), residues: 857 sheet: -1.24 (0.75), residues: 50 loop : -2.08 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 176 HIS 0.002 0.001 HIS A 242 PHE 0.012 0.001 PHE A 494 TYR 0.023 0.001 TYR A 381 ARG 0.007 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 653) hydrogen bonds : angle 4.21254 ( 1929) covalent geometry : bond 0.00246 (11035) covalent geometry : angle 0.52286 (15026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.242 Fit side-chains REVERT: A 225 ILE cc_start: 0.9194 (tp) cc_final: 0.8951 (tp) REVERT: A 366 MET cc_start: 0.8779 (ttm) cc_final: 0.8384 (ttm) REVERT: B 36 MET cc_start: 0.7375 (mmt) cc_final: 0.7101 (mmt) REVERT: B 101 LYS cc_start: 0.6725 (mtmm) cc_final: 0.6095 (pptt) REVERT: B 131 ILE cc_start: 0.6880 (tp) cc_final: 0.6597 (tt) REVERT: B 186 TRP cc_start: 0.2649 (p-90) cc_final: 0.2384 (p-90) REVERT: B 306 LEU cc_start: 0.8858 (mt) cc_final: 0.8505 (mt) REVERT: B 383 MET cc_start: 0.6335 (ppp) cc_final: 0.5905 (tpp) REVERT: B 465 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7758 (mp) outliers start: 16 outliers final: 12 residues processed: 163 average time/residue: 0.2015 time to fit residues: 49.2453 Evaluate side-chains 157 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 129 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115143 restraints weight = 17121.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117247 restraints weight = 9253.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118598 restraints weight = 6250.519| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11035 Z= 0.116 Angle : 0.522 7.194 15026 Z= 0.260 Chirality : 0.039 0.147 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.395 113.329 1537 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.12 % Allowed : 15.96 % Favored : 81.92 % 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: 0.30 (0.22), residues: 1439 helix: 1.56 (0.18), residues: 850 sheet: -1.16 (0.75), residues: 50 loop : -1.98 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 176 HIS 0.002 0.001 HIS A 242 PHE 0.016 0.001 PHE A 327 TYR 0.022 0.001 TYR A 381 ARG 0.006 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 653) hydrogen bonds : angle 4.20174 ( 1929) covalent geometry : bond 0.00259 (11035) covalent geometry : angle 0.52242 (15026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.132 Fit side-chains REVERT: A 225 ILE cc_start: 0.9244 (tp) cc_final: 0.9005 (tp) REVERT: A 366 MET cc_start: 0.8805 (ttm) cc_final: 0.8401 (ttm) REVERT: A 389 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7751 (mp) REVERT: B 131 ILE cc_start: 0.6894 (tp) cc_final: 0.6593 (tt) REVERT: B 383 MET cc_start: 0.6277 (ppp) cc_final: 0.5913 (tpp) REVERT: B 465 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7719 (mp) outliers start: 24 outliers final: 18 residues processed: 163 average time/residue: 0.2107 time to fit residues: 51.5062 Evaluate side-chains 164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 681 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 118 optimal weight: 40.0000 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN B 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116053 restraints weight = 17197.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116797 restraints weight = 9531.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117554 restraints weight = 6650.505| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11035 Z= 0.118 Angle : 0.523 6.739 15026 Z= 0.260 Chirality : 0.039 0.147 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.326 112.361 1537 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.20 % Allowed : 17.02 % Favored : 80.78 % 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: 0.30 (0.22), residues: 1439 helix: 1.59 (0.18), residues: 850 sheet: -1.56 (0.68), residues: 60 loop : -1.99 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 176 HIS 0.002 0.001 HIS A 242 PHE 0.013 0.001 PHE A 494 TYR 0.022 0.001 TYR A 381 ARG 0.007 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 653) hydrogen bonds : angle 4.20660 ( 1929) covalent geometry : bond 0.00264 (11035) covalent geometry : angle 0.52272 (15026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.060 Fit side-chains REVERT: A 225 ILE cc_start: 0.9205 (tp) cc_final: 0.8963 (tp) REVERT: A 366 MET cc_start: 0.8715 (ttm) cc_final: 0.8240 (ttm) REVERT: A 389 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7757 (mp) REVERT: B 131 ILE cc_start: 0.6864 (tp) cc_final: 0.6595 (tt) REVERT: B 383 MET cc_start: 0.6387 (ppp) cc_final: 0.5913 (tpp) REVERT: B 465 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7792 (mp) outliers start: 25 outliers final: 20 residues processed: 164 average time/residue: 0.2166 time to fit residues: 53.4539 Evaluate side-chains 164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 681 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 129 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** 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 = 0.3735 r_free = 0.3735 target = 0.141629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112361 restraints weight = 17054.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114492 restraints weight = 9152.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115631 restraints weight = 6159.983| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11035 Z= 0.143 Angle : 0.543 6.174 15026 Z= 0.271 Chirality : 0.040 0.151 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.368 112.112 1537 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.38 % Allowed : 17.20 % Favored : 80.42 % 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: 0.24 (0.22), residues: 1439 helix: 1.56 (0.18), residues: 849 sheet: -1.56 (0.68), residues: 60 loop : -2.04 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 176 HIS 0.003 0.001 HIS A 351 PHE 0.014 0.001 PHE A 494 TYR 0.021 0.001 TYR A 381 ARG 0.005 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 653) hydrogen bonds : angle 4.27665 ( 1929) covalent geometry : bond 0.00329 (11035) covalent geometry : angle 0.54348 (15026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.103 Fit side-chains REVERT: A 225 ILE cc_start: 0.9197 (tp) cc_final: 0.8973 (tp) REVERT: A 366 MET cc_start: 0.8799 (ttm) cc_final: 0.8327 (ttm) REVERT: B 131 ILE cc_start: 0.6921 (tp) cc_final: 0.6615 (tt) REVERT: B 383 MET cc_start: 0.6259 (ppp) cc_final: 0.5816 (tpp) REVERT: B 465 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7808 (mp) outliers start: 27 outliers final: 21 residues processed: 163 average time/residue: 0.1971 time to fit residues: 48.5117 Evaluate side-chains 164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 681 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 142 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 130 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 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 = 0.3757 r_free = 0.3757 target = 0.143503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114407 restraints weight = 17242.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116605 restraints weight = 9115.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117755 restraints weight = 6057.304| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11035 Z= 0.113 Angle : 0.532 6.161 15026 Z= 0.265 Chirality : 0.039 0.159 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.316 111.628 1537 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.12 % Allowed : 17.64 % Favored : 80.25 % 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: 0.34 (0.22), residues: 1439 helix: 1.64 (0.18), residues: 850 sheet: -1.47 (0.68), residues: 60 loop : -2.02 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 176 HIS 0.002 0.001 HIS A 242 PHE 0.022 0.001 PHE A 327 TYR 0.022 0.001 TYR A 381 ARG 0.005 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 653) hydrogen bonds : angle 4.22569 ( 1929) covalent geometry : bond 0.00249 (11035) covalent geometry : angle 0.53155 (15026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.096 Fit side-chains REVERT: A 225 ILE cc_start: 0.9157 (tp) cc_final: 0.8921 (tp) REVERT: A 316 SER cc_start: 0.8691 (t) cc_final: 0.8479 (p) REVERT: A 366 MET cc_start: 0.8736 (ttm) cc_final: 0.8274 (ttm) REVERT: B 131 ILE cc_start: 0.6925 (tp) cc_final: 0.6631 (tt) REVERT: B 383 MET cc_start: 0.6236 (ppp) cc_final: 0.5844 (tpp) REVERT: B 465 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7751 (mp) outliers start: 24 outliers final: 18 residues processed: 164 average time/residue: 0.1943 time to fit residues: 47.6323 Evaluate side-chains 164 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 59 optimal weight: 0.0010 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 129 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** 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 = 0.3758 r_free = 0.3758 target = 0.143552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114514 restraints weight = 16946.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116644 restraints weight = 9033.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118035 restraints weight = 6067.926| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11035 Z= 0.114 Angle : 0.534 5.959 15026 Z= 0.267 Chirality : 0.039 0.180 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.284 110.838 1537 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.68 % Allowed : 17.99 % Favored : 80.34 % 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: 0.36 (0.22), residues: 1439 helix: 1.67 (0.18), residues: 849 sheet: -1.39 (0.69), residues: 60 loop : -2.05 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 176 HIS 0.003 0.001 HIS A 242 PHE 0.020 0.001 PHE A 327 TYR 0.023 0.001 TYR A 381 ARG 0.005 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 653) hydrogen bonds : angle 4.20958 ( 1929) covalent geometry : bond 0.00251 (11035) covalent geometry : angle 0.53440 (15026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.112 Fit side-chains REVERT: A 225 ILE cc_start: 0.9153 (tp) cc_final: 0.8901 (tp) REVERT: A 366 MET cc_start: 0.8739 (ttm) cc_final: 0.8288 (ttm) REVERT: B 131 ILE cc_start: 0.6869 (tp) cc_final: 0.6557 (tt) REVERT: B 383 MET cc_start: 0.6223 (ppp) cc_final: 0.5869 (tpp) REVERT: B 465 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7784 (mp) outliers start: 19 outliers final: 17 residues processed: 159 average time/residue: 0.1980 time to fit residues: 47.1276 Evaluate side-chains 162 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 129 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** 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 = 0.3761 r_free = 0.3761 target = 0.143848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116377 restraints weight = 16905.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116455 restraints weight = 10753.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116847 restraints weight = 8540.521| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11035 Z= 0.112 Angle : 0.536 8.546 15026 Z= 0.267 Chirality : 0.039 0.190 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.265 110.392 1537 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.94 % Allowed : 17.81 % Favored : 80.25 % 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: 0.40 (0.22), residues: 1439 helix: 1.71 (0.18), residues: 848 sheet: -1.36 (0.70), residues: 60 loop : -2.04 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 176 HIS 0.003 0.001 HIS A 242 PHE 0.019 0.001 PHE A 327 TYR 0.024 0.001 TYR A 381 ARG 0.005 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 653) hydrogen bonds : angle 4.19278 ( 1929) covalent geometry : bond 0.00245 (11035) covalent geometry : angle 0.53563 (15026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3453.46 seconds wall clock time: 61 minutes 57.08 seconds (3717.08 seconds total)