Starting phenix.real_space_refine on Sat Jul 20 13:12:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/07_2024/7zrm_14919_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/07_2024/7zrm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/07_2024/7zrm_14919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/07_2024/7zrm_14919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/07_2024/7zrm_14919_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrm_14919/07_2024/7zrm_14919_neut.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 Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.52, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 4.48 Conformation dependent library (CDL) restraints added in 2.2 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: 1.11 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: 3.38 Time building geometry restraints manager: 4.70 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: 99.62 - 106.92: 351 106.92 - 114.21: 6504 114.21 - 121.51: 5639 121.51 - 128.80: 2460 128.80 - 136.10: 72 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 2.440 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.265 2.440 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.265 2.440 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR A 113 " pdb=" OD1 ASN A 466 " model vdw 2.305 2.440 ... (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 ========== 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: 0.610 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 33.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.930 ------------------------------------------------------------------------------- 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= 0.273 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.396 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: 0.2044 time to fit residues: 55.8017 Evaluate side-chains 150 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 10.0000 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 231 ASN B 459 GLN B 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11035 Z= 0.223 Angle : 0.562 6.358 15026 Z= 0.281 Chirality : 0.040 0.157 1811 Planarity : 0.005 0.055 1902 Dihedral : 5.771 110.493 1537 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.88 % Allowed : 10.23 % Favored : 88.89 % 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: -0.46 (0.22), residues: 1439 helix: 0.87 (0.17), residues: 855 sheet: -1.21 (0.75), residues: 50 loop : -2.20 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.002 0.001 HIS A 351 PHE 0.015 0.001 PHE A 373 TYR 0.027 0.001 TYR A 381 ARG 0.004 0.000 ARG A 44 *********************** 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 168 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.112 Fit side-chains REVERT: C 130 ASN cc_start: 0.7834 (t0) cc_final: 0.7143 (t0) REVERT: C 170 TYR cc_start: 0.6987 (p90) cc_final: 0.6655 (p90) REVERT: B 203 MET cc_start: 0.6366 (ptt) cc_final: 0.6153 (ptt) REVERT: B 383 MET cc_start: 0.6036 (ppp) cc_final: 0.5511 (tpp) outliers start: 10 outliers final: 9 residues processed: 161 average time/residue: 0.1926 time to fit residues: 47.0020 Evaluate side-chains 156 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 411 HIS 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 72 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 0.0470 chunk 104 optimal weight: 0.9980 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 319 ASN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 540 GLN B 563 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11035 Z= 0.365 Angle : 0.639 8.448 15026 Z= 0.321 Chirality : 0.043 0.172 1811 Planarity : 0.005 0.053 1902 Dihedral : 5.982 112.290 1537 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.82 % Allowed : 13.49 % Favored : 83.69 % 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: -0.41 (0.22), residues: 1439 helix: 0.94 (0.18), residues: 849 sheet: -1.74 (0.66), residues: 60 loop : -2.14 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 176 HIS 0.005 0.001 HIS A 351 PHE 0.018 0.002 PHE A 373 TYR 0.024 0.002 TYR A 381 ARG 0.006 0.000 ARG B 572 *********************** 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 175 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.062 Fit side-chains REVERT: A 114 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7867 (t0) REVERT: C 130 ASN cc_start: 0.8044 (t0) cc_final: 0.7328 (t0) REVERT: B 36 MET cc_start: 0.7378 (mmt) cc_final: 0.7104 (mmt) REVERT: B 131 ILE cc_start: 0.6773 (tp) cc_final: 0.6487 (tt) REVERT: B 183 LEU cc_start: 0.6010 (mp) cc_final: 0.4910 (tp) REVERT: B 383 MET cc_start: 0.6415 (ppp) cc_final: 0.5732 (tpp) REVERT: B 411 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6565 (t-90) outliers start: 32 outliers final: 20 residues processed: 160 average time/residue: 0.1821 time to fit residues: 44.5616 Evaluate side-chains 156 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 140 ILE 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 411 HIS Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 679 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 367 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11035 Z= 0.191 Angle : 0.540 6.442 15026 Z= 0.269 Chirality : 0.039 0.161 1811 Planarity : 0.004 0.052 1902 Dihedral : 5.770 112.203 1537 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.68 % Allowed : 16.93 % Favored : 81.39 % 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: -0.06 (0.22), residues: 1439 helix: 1.25 (0.18), residues: 854 sheet: -1.40 (0.75), residues: 50 loop : -2.10 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 176 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 373 TYR 0.027 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** 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 166 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.111 Fit side-chains REVERT: A 114 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7912 (t0) REVERT: A 366 MET cc_start: 0.8883 (ttm) cc_final: 0.8604 (ttm) REVERT: C 130 ASN cc_start: 0.7990 (t0) cc_final: 0.7251 (t0) REVERT: B 36 MET cc_start: 0.7273 (mmt) cc_final: 0.6979 (mmt) REVERT: B 131 ILE cc_start: 0.6796 (tp) cc_final: 0.6496 (tt) REVERT: B 383 MET cc_start: 0.6176 (ppp) cc_final: 0.5733 (tpp) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 0.1881 time to fit residues: 46.1948 Evaluate side-chains 151 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 LEU 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 411 HIS 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 115 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11035 Z= 0.396 Angle : 0.655 7.624 15026 Z= 0.330 Chirality : 0.044 0.199 1811 Planarity : 0.005 0.053 1902 Dihedral : 6.045 111.877 1537 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.53 % Allowed : 17.90 % Favored : 78.57 % 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: -0.40 (0.22), residues: 1439 helix: 0.94 (0.17), residues: 855 sheet: -1.75 (0.67), residues: 60 loop : -2.16 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 176 HIS 0.004 0.001 HIS A 351 PHE 0.022 0.002 PHE A 373 TYR 0.020 0.002 TYR A 381 ARG 0.006 0.000 ARG B 572 *********************** 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 174 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.181 Fit side-chains REVERT: A 114 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7950 (t0) REVERT: C 130 ASN cc_start: 0.8213 (t0) cc_final: 0.7665 (t0) REVERT: B 36 MET cc_start: 0.7376 (mmt) cc_final: 0.7096 (mmt) REVERT: B 131 ILE cc_start: 0.6829 (tp) cc_final: 0.6544 (tt) REVERT: B 411 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6703 (t-90) REVERT: B 535 MET cc_start: 0.7939 (tpp) cc_final: 0.7615 (tpp) REVERT: B 608 MET cc_start: 0.8044 (mtm) cc_final: 0.7597 (mtm) outliers start: 40 outliers final: 25 residues processed: 162 average time/residue: 0.1841 time to fit residues: 46.2561 Evaluate side-chains 153 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 140 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 236 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 LEU 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 46 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2198 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= 0.181 Angle : 0.555 8.134 15026 Z= 0.275 Chirality : 0.040 0.152 1811 Planarity : 0.004 0.050 1902 Dihedral : 5.662 110.314 1537 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.94 % Allowed : 19.93 % Favored : 78.13 % 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: -0.02 (0.22), residues: 1439 helix: 1.33 (0.18), residues: 852 sheet: -1.61 (0.67), residues: 60 loop : -2.14 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 186 HIS 0.007 0.001 HIS A 451 PHE 0.010 0.001 PHE B 623 TYR 0.029 0.002 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** 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 166 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.176 Fit side-chains REVERT: A 129 GLN cc_start: 0.8327 (mt0) cc_final: 0.8045 (mt0) REVERT: A 366 MET cc_start: 0.8758 (ttm) cc_final: 0.8480 (ttm) REVERT: C 130 ASN cc_start: 0.8092 (t0) cc_final: 0.7287 (t0) REVERT: B 131 ILE cc_start: 0.6824 (tp) cc_final: 0.6491 (tt) REVERT: B 383 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.4907 (tpp) REVERT: B 608 MET cc_start: 0.8197 (mtm) cc_final: 0.7772 (mtm) outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.1865 time to fit residues: 44.1647 Evaluate side-chains 148 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 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 383 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 86 optimal weight: 0.0970 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2151 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= 0.172 Angle : 0.549 6.997 15026 Z= 0.271 Chirality : 0.039 0.154 1811 Planarity : 0.004 0.045 1902 Dihedral : 5.439 108.638 1537 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.76 % Allowed : 20.28 % Favored : 77.95 % 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: 0.15 (0.22), residues: 1439 helix: 1.52 (0.18), residues: 849 sheet: -1.83 (0.62), residues: 70 loop : -2.11 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 186 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 373 TYR 0.032 0.001 TYR A 381 ARG 0.004 0.000 ARG A 44 *********************** 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 164 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.032 Fit side-chains REVERT: A 129 GLN cc_start: 0.8176 (mt0) cc_final: 0.7904 (mt0) REVERT: A 366 MET cc_start: 0.8781 (ttm) cc_final: 0.8527 (ttm) REVERT: C 130 ASN cc_start: 0.8003 (t0) cc_final: 0.7149 (t0) REVERT: B 53 MET cc_start: 0.7502 (ttt) cc_final: 0.7047 (ttt) REVERT: B 131 ILE cc_start: 0.6847 (tp) cc_final: 0.6502 (tt) REVERT: B 383 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.4885 (tpp) REVERT: B 608 MET cc_start: 0.8062 (mtm) cc_final: 0.7715 (mtm) outliers start: 20 outliers final: 13 residues processed: 158 average time/residue: 0.1797 time to fit residues: 43.5775 Evaluate side-chains 153 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 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 383 MET Chi-restraints excluded: chain B residue 549 VAL 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 55 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11035 Z= 0.212 Angle : 0.565 6.954 15026 Z= 0.280 Chirality : 0.040 0.191 1811 Planarity : 0.004 0.046 1902 Dihedral : 5.461 107.789 1537 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.59 % Allowed : 20.28 % Favored : 78.13 % 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: 0.13 (0.22), residues: 1439 helix: 1.51 (0.18), residues: 850 sheet: -1.85 (0.62), residues: 70 loop : -2.13 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 186 HIS 0.003 0.001 HIS A 451 PHE 0.013 0.001 PHE A 373 TYR 0.026 0.001 TYR A 381 ARG 0.003 0.000 ARG B 572 *********************** 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 160 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.232 Fit side-chains REVERT: A 129 GLN cc_start: 0.8264 (mt0) cc_final: 0.7974 (mt0) REVERT: A 225 ILE cc_start: 0.9146 (tp) cc_final: 0.8882 (tp) REVERT: A 366 MET cc_start: 0.8826 (ttm) cc_final: 0.8561 (ttm) REVERT: C 130 ASN cc_start: 0.8049 (t0) cc_final: 0.7171 (t0) REVERT: B 53 MET cc_start: 0.7607 (ttt) cc_final: 0.7157 (ttt) REVERT: B 131 ILE cc_start: 0.6811 (tp) cc_final: 0.6485 (tt) REVERT: B 383 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.4905 (tpp) REVERT: B 411 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6863 (t-90) REVERT: B 608 MET cc_start: 0.8089 (mtm) cc_final: 0.7787 (mtm) outliers start: 18 outliers final: 16 residues processed: 154 average time/residue: 0.1871 time to fit residues: 44.4326 Evaluate side-chains 159 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 LEU 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 383 MET Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 618 LEU 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 132 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 0.0870 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11035 Z= 0.162 Angle : 0.547 6.582 15026 Z= 0.271 Chirality : 0.039 0.146 1811 Planarity : 0.004 0.045 1902 Dihedral : 5.366 107.179 1537 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.50 % Allowed : 20.72 % Favored : 77.78 % 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: 0.26 (0.22), residues: 1439 helix: 1.54 (0.18), residues: 861 sheet: -1.59 (0.68), residues: 60 loop : -2.06 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 176 HIS 0.013 0.001 HIS B 563 PHE 0.010 0.001 PHE A 109 TYR 0.029 0.001 TYR A 381 ARG 0.003 0.000 ARG B 572 *********************** 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 164 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.246 Fit side-chains REVERT: A 129 GLN cc_start: 0.8253 (mt0) cc_final: 0.7966 (mt0) REVERT: A 225 ILE cc_start: 0.9147 (tp) cc_final: 0.8872 (tp) REVERT: A 357 LEU cc_start: 0.7931 (tt) cc_final: 0.7525 (tt) REVERT: A 366 MET cc_start: 0.8784 (ttm) cc_final: 0.8526 (ttm) REVERT: C 130 ASN cc_start: 0.8043 (t0) cc_final: 0.7196 (t0) REVERT: B 53 MET cc_start: 0.7547 (ttt) cc_final: 0.7132 (ttt) REVERT: B 131 ILE cc_start: 0.6817 (tp) cc_final: 0.6490 (tt) REVERT: B 383 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.4951 (tpp) REVERT: B 411 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6857 (t-90) REVERT: B 608 MET cc_start: 0.8069 (mtm) cc_final: 0.7714 (mtm) outliers start: 17 outliers final: 15 residues processed: 158 average time/residue: 0.2039 time to fit residues: 49.3582 Evaluate side-chains 160 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 541 LEU 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 383 MET Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 618 LEU 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 135 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 90 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11035 Z= 0.153 Angle : 0.539 6.963 15026 Z= 0.266 Chirality : 0.039 0.161 1811 Planarity : 0.004 0.045 1902 Dihedral : 5.236 105.144 1537 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.32 % Allowed : 20.99 % Favored : 77.69 % 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: 1.74 (0.18), residues: 846 sheet: -1.61 (0.59), residues: 70 loop : -2.03 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 176 HIS 0.005 0.001 HIS B 563 PHE 0.011 0.001 PHE A 373 TYR 0.029 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 ********************** 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 163 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.245 Fit side-chains REVERT: A 129 GLN cc_start: 0.8314 (mt0) cc_final: 0.8014 (mt0) REVERT: A 225 ILE cc_start: 0.9186 (tp) cc_final: 0.8938 (tp) REVERT: A 366 MET cc_start: 0.8769 (ttm) cc_final: 0.8531 (ttm) REVERT: C 130 ASN cc_start: 0.7993 (t0) cc_final: 0.7209 (t0) REVERT: B 53 MET cc_start: 0.7564 (ttt) cc_final: 0.7119 (ttt) REVERT: B 131 ILE cc_start: 0.6803 (tp) cc_final: 0.6476 (tt) REVERT: B 383 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.4969 (tpp) REVERT: B 411 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: B 608 MET cc_start: 0.7995 (mtm) cc_final: 0.7698 (mtm) outliers start: 15 outliers final: 13 residues processed: 156 average time/residue: 0.1917 time to fit residues: 45.1368 Evaluate side-chains 159 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 46 THR 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 383 MET Chi-restraints excluded: chain B residue 411 HIS 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 120 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 113 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113721 restraints weight = 16960.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114589 restraints weight = 10310.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115234 restraints weight = 6882.043| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11035 Z= 0.155 Angle : 0.540 8.561 15026 Z= 0.265 Chirality : 0.039 0.147 1811 Planarity : 0.004 0.045 1902 Dihedral : 5.178 104.216 1537 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.68 % Allowed : 20.99 % Favored : 77.34 % 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: 0.47 (0.22), residues: 1439 helix: 1.78 (0.18), residues: 845 sheet: -1.54 (0.60), residues: 70 loop : -1.99 (0.25), residues: 524 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 0.024 0.001 PHE A 327 TYR 0.028 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.81 seconds wall clock time: 36 minutes 39.32 seconds (2199.32 seconds total)