Starting phenix.real_space_refine on Thu Aug 6 09:01:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8j_39848/08_2026/8z8j_39848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8j_39848/08_2026/8z8j_39848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z8j_39848/08_2026/8z8j_39848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8j_39848/08_2026/8z8j_39848.map" model { file = "/net/cci-nas-00/data/ceres_data/8z8j_39848/08_2026/8z8j_39848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8j_39848/08_2026/8z8j_39848.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 80 5.16 5 C 8698 2.51 5 N 2387 2.21 5 O 2587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13766 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5021 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5255 Classifications: {'peptide': 656} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 622} Chain breaks: 3 Chain: "C" Number of atoms: 3170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3158 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 27, 'TRANS': 360} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 388, 3158 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 27, 'TRANS': 360} Chain breaks: 3 bond proxies already assigned to first conformer: 3228 Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER C 336 " occ=0.39 ... (10 atoms not shown) pdb=" OG BSER C 336 " occ=0.61 residue: pdb=" N ASER C 384 " occ=0.01 ... (10 atoms not shown) pdb=" OG BSER C 384 " occ=0.99 Time building chain proxies: 3.43, per 1000 atoms: 0.25 Number of scatterers: 13766 At special positions: 0 Unit cell: (89.8461, 101.526, 137.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 14 15.00 O 2587 8.00 N 2387 7.00 C 8698 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: 0.98 Conformation dependent library (CDL) restraints added in 636.3 milliseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 47.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 4.547A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.548A pdb=" N ASP A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.631A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.734A pdb=" N ILE A 298 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.958A pdb=" N SER A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.165A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.494A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.531A pdb=" N SER A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 516 removed outlier: 4.014A pdb=" N ASN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.509A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.758A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.641A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.792A pdb=" N LYS B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.615A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.494A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.782A pdb=" N ALA B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.538A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS B 308 " --> pdb=" O PHE B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.937A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.554A pdb=" N PHE B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.604A pdb=" N THR B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.600A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.598A pdb=" N ALA B 502 " --> pdb=" O MET B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.547A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.707A pdb=" N GLU B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 646 through 666 removed outlier: 4.103A pdb=" N ASN B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 709 Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.660A pdb=" N ARG C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.195A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 191 through 207 Proline residue: C 202 - end of helix removed outlier: 3.620A pdb=" N LYS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.575A pdb=" N GLU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 415 removed outlier: 3.619A pdb=" N GLY C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.957A pdb=" N GLY C 420 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 removed outlier: 3.607A pdb=" N PHE C 435 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 455 removed outlier: 3.555A pdb=" N LEU C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.524A pdb=" N LYS A 97 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 119 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.681A pdb=" N GLY B 300 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.823A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.761A pdb=" N ILE A 414 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET A 428 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS A 412 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 430 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR A 410 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.537A pdb=" N SER B 126 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 removed outlier: 3.796A pdb=" N ASN B 227 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB5, first strand: chain 'C' and resid 348 through 354 removed outlier: 3.510A pdb=" N LYS C 349 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 353 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 370 through 376 removed outlier: 4.319A pdb=" N GLU C 392 " --> pdb=" O ASER C 384 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR C 482 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 393 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 456 through 457 removed outlier: 3.520A pdb=" N LYS C 477 " --> pdb=" O ASP C 457 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1612 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: 2.37 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4411 1.34 - 1.46: 2420 1.46 - 1.58: 7123 1.58 - 1.70: 27 1.70 - 1.82: 129 Bond restraints: 14110 Sorted by residual: bond pdb=" CB PRO C 343 " pdb=" CG PRO C 343 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.23e+00 bond pdb=" CB LYS C 458 " pdb=" CG LYS C 458 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" C GLU C 418 " pdb=" N PRO C 419 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.90e-01 bond pdb=" CA ASN A 156 " pdb=" CB ASN A 156 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.77e-01 bond pdb=" CB ASN C 80 " pdb=" CG ASN C 80 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.48e-01 ... (remaining 14105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18879 2.04 - 4.08: 256 4.08 - 6.13: 27 6.13 - 8.17: 6 8.17 - 10.21: 2 Bond angle restraints: 19170 Sorted by residual: angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 112.96 107.93 5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" O5' A D 7 " pdb=" C5' A D 7 " pdb=" C4' A D 7 " ideal model delta sigma weight residual 109.40 112.38 -2.98 8.00e-01 1.56e+00 1.39e+01 angle pdb=" C ASN A 155 " pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 121.54 127.88 -6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" O5' C E 16 " pdb=" C5' C E 16 " pdb=" C4' C E 16 " ideal model delta sigma weight residual 109.40 112.05 -2.65 8.00e-01 1.56e+00 1.10e+01 angle pdb=" CA PRO C 343 " pdb=" N PRO C 343 " pdb=" CD PRO C 343 " ideal model delta sigma weight residual 112.00 107.49 4.51 1.40e+00 5.10e-01 1.04e+01 ... (remaining 19165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7820 17.95 - 35.90: 641 35.90 - 53.85: 103 53.85 - 71.80: 30 71.80 - 89.75: 11 Dihedral angle restraints: 8605 sinusoidal: 3706 harmonic: 4899 Sorted by residual: dihedral pdb=" CA GLU C 418 " pdb=" C GLU C 418 " pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta harmonic sigma weight residual 180.00 -162.13 -17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB GLU B 372 " pdb=" CG GLU B 372 " pdb=" CD GLU B 372 " pdb=" OE1 GLU B 372 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 550 " pdb=" CG GLU B 550 " pdb=" CD GLU B 550 " pdb=" OE1 GLU B 550 " ideal model delta sinusoidal sigma weight residual 0.00 -88.89 88.89 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1371 0.032 - 0.064: 512 0.064 - 0.095: 171 0.095 - 0.127: 65 0.127 - 0.159: 16 Chirality restraints: 2135 Sorted by residual: chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ASN A 156 " pdb=" N ASN A 156 " pdb=" C ASN A 156 " pdb=" CB ASN A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLU C 405 " pdb=" N GLU C 405 " pdb=" C GLU C 405 " pdb=" CB GLU C 405 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 2132 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 342 " 0.046 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO C 343 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 234 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C 235 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 97 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.032 5.00e-02 4.00e+02 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1765 2.75 - 3.29: 13745 3.29 - 3.83: 23114 3.83 - 4.36: 27698 4.36 - 4.90: 47543 Nonbonded interactions: 113865 Sorted by model distance: nonbonded pdb=" O SER A 482 " pdb=" O2' A D 3 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 295 " pdb=" O PRO B 464 " model vdw 2.256 3.040 nonbonded pdb=" ND2 ASN A 558 " pdb=" O PRO B 25 " model vdw 2.256 3.120 nonbonded pdb=" O ILE C 122 " pdb=" NE2 GLN C 207 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR B 245 " pdb=" NH2 ARG B 251 " model vdw 2.268 3.120 ... (remaining 113860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.450 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.002 0.075 14110 Z= 0.108 Angle : 0.558 10.211 19170 Z= 0.292 Chirality : 0.041 0.159 2135 Planarity : 0.005 0.067 2401 Dihedral : 13.582 89.746 5423 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1653 helix: 1.02 (0.20), residues: 721 sheet: -0.55 (0.40), residues: 172 loop : -1.25 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 704 TYR 0.023 0.001 TYR B 176 PHE 0.029 0.001 PHE B 290 TRP 0.011 0.001 TRP B 220 HIS 0.007 0.001 HIS C 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (14110) covalent geometry : angle 0.55850 / 0.29 (19170) hydrogen bonds : bond 0.18599 / 12.84 ( 578) hydrogen bonds : angle 6.39146 / 4.30 ( 1612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8160 (t0) cc_final: 0.6862 (t0) REVERT: A 83 ASP cc_start: 0.7768 (m-30) cc_final: 0.7518 (m-30) REVERT: A 163 GLU cc_start: 0.8831 (tp30) cc_final: 0.8510 (tp30) REVERT: A 447 ILE cc_start: 0.9270 (mm) cc_final: 0.9052 (mm) REVERT: B 393 MET cc_start: 0.7460 (tpt) cc_final: 0.6911 (tpt) REVERT: B 422 ASP cc_start: 0.7992 (p0) cc_final: 0.7783 (p0) REVERT: B 653 GLU cc_start: 0.8184 (mp0) cc_final: 0.7647 (mp0) REVERT: C 378 GLN cc_start: 0.8881 (mm110) cc_final: 0.8523 (mm110) REVERT: C 405 GLU cc_start: 0.7240 (pp20) cc_final: 0.6954 (pp20) REVERT: C 410 ILE cc_start: 0.8818 (mt) cc_final: 0.8552 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1157 time to fit residues: 37.6671 Evaluate side-chains 188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 129 HIS B 336 ASN B 453 ASN ** B 482 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 = 0.3655 r_free = 0.3655 target = 0.126668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095740 restraints weight = 48215.023| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.74 r_work: 0.3013 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14110 Z= 0.127 Angle : 0.572 8.924 19170 Z= 0.292 Chirality : 0.041 0.161 2135 Planarity : 0.005 0.060 2401 Dihedral : 8.421 73.469 2033 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.60 % Allowed : 6.74 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1653 helix: 1.16 (0.20), residues: 729 sheet: -0.75 (0.37), residues: 190 loop : -1.20 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 704 TYR 0.026 0.001 TYR C 382 PHE 0.018 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS C 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14110) covalent geometry : angle 0.57247 / 0.29 (19170) hydrogen bonds : bond 0.04477 / 3.15 ( 578) hydrogen bonds : angle 5.04887 / 3.45 ( 1612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 0.551 Fit side-chains REVERT: A 47 ASN cc_start: 0.8591 (t0) cc_final: 0.8214 (t0) REVERT: A 48 MET cc_start: 0.7941 (ppp) cc_final: 0.7738 (ppp) REVERT: A 163 GLU cc_start: 0.8929 (tp30) cc_final: 0.8516 (tp30) REVERT: A 621 TYR cc_start: 0.8446 (m-80) cc_final: 0.8044 (m-80) REVERT: B 283 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8315 (tppt) REVERT: B 393 MET cc_start: 0.7973 (tpt) cc_final: 0.7338 (tpt) REVERT: B 409 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 653 GLU cc_start: 0.8543 (mp0) cc_final: 0.8012 (mp0) REVERT: C 377 ASP cc_start: 0.8671 (t0) cc_final: 0.8194 (t0) REVERT: C 378 GLN cc_start: 0.8853 (mm110) cc_final: 0.8490 (mm110) REVERT: C 405 GLU cc_start: 0.7353 (pp20) cc_final: 0.7060 (pp20) REVERT: C 410 ILE cc_start: 0.8875 (mt) cc_final: 0.8639 (mt) outliers start: 9 outliers final: 9 residues processed: 214 average time/residue: 0.1235 time to fit residues: 38.6730 Evaluate side-chains 188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 156 optimal weight: 30.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 HIS ** 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 = 0.3579 r_free = 0.3579 target = 0.120899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089039 restraints weight = 53939.494| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.85 r_work: 0.2889 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14110 Z= 0.240 Angle : 0.622 7.352 19170 Z= 0.317 Chirality : 0.044 0.212 2135 Planarity : 0.005 0.060 2401 Dihedral : 8.550 73.383 2033 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.34 % Allowed : 8.68 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.21), residues: 1653 helix: 1.13 (0.20), residues: 736 sheet: -1.09 (0.37), residues: 170 loop : -1.17 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 93 TYR 0.032 0.002 TYR C 363 PHE 0.018 0.002 PHE C 374 TRP 0.013 0.001 TRP A 336 HIS 0.006 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (14110) covalent geometry : angle 0.62236 / 0.32 (19170) hydrogen bonds : bond 0.04491 / 3.09 ( 578) hydrogen bonds : angle 4.86265 / 3.36 ( 1612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.461 Fit side-chains REVERT: A 47 ASN cc_start: 0.8650 (t0) cc_final: 0.8009 (t0) REVERT: A 163 GLU cc_start: 0.8952 (tp30) cc_final: 0.8565 (tp30) REVERT: A 365 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: B 248 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8426 (mmt) REVERT: B 393 MET cc_start: 0.8043 (tpt) cc_final: 0.7597 (tpt) REVERT: B 422 ASP cc_start: 0.8603 (p0) cc_final: 0.8346 (p0) REVERT: B 653 GLU cc_start: 0.8510 (mp0) cc_final: 0.7987 (mp0) REVERT: B 686 ARG cc_start: 0.8729 (mmt-90) cc_final: 0.8488 (mmm160) REVERT: C 210 GLU cc_start: 0.7970 (mp0) cc_final: 0.7655 (mp0) outliers start: 20 outliers final: 11 residues processed: 204 average time/residue: 0.1325 time to fit residues: 38.6976 Evaluate side-chains 198 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 79 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091279 restraints weight = 47152.450| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.65 r_work: 0.2938 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14110 Z= 0.129 Angle : 0.558 7.814 19170 Z= 0.281 Chirality : 0.041 0.158 2135 Planarity : 0.004 0.059 2401 Dihedral : 8.487 73.399 2033 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.40 % Allowed : 10.61 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1653 helix: 1.27 (0.20), residues: 735 sheet: -1.15 (0.36), residues: 170 loop : -1.13 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 704 TYR 0.023 0.001 TYR C 363 PHE 0.018 0.001 PHE C 374 TRP 0.012 0.001 TRP A 336 HIS 0.005 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14110) covalent geometry : angle 0.55827 / 0.28 (19170) hydrogen bonds : bond 0.03733 / 2.57 ( 578) hydrogen bonds : angle 4.61672 / 3.19 ( 1612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9047 (mmtm) cc_final: 0.8774 (mmtm) REVERT: A 163 GLU cc_start: 0.8937 (tp30) cc_final: 0.8528 (tp30) REVERT: A 365 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: A 437 LYS cc_start: 0.8687 (ptpt) cc_final: 0.8482 (mttt) REVERT: A 451 MET cc_start: 0.9258 (mtt) cc_final: 0.8812 (mtt) REVERT: B 283 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8373 (tppt) REVERT: B 422 ASP cc_start: 0.8522 (p0) cc_final: 0.8273 (p0) REVERT: B 503 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8274 (mpp) REVERT: B 686 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8454 (mmm160) REVERT: C 142 ARG cc_start: 0.8645 (ptm-80) cc_final: 0.8387 (ptm-80) REVERT: C 371 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8612 (tppt) outliers start: 21 outliers final: 12 residues processed: 202 average time/residue: 0.1166 time to fit residues: 34.1757 Evaluate side-chains 195 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 102 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 429 ASN B 433 HIS ** C 249 HIS ** 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 = 0.3587 r_free = 0.3587 target = 0.121411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090169 restraints weight = 48413.196| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.81 r_work: 0.2902 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14110 Z= 0.172 Angle : 0.575 8.287 19170 Z= 0.290 Chirality : 0.042 0.183 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.487 73.389 2033 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.47 % Allowed : 10.75 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1653 helix: 1.28 (0.20), residues: 735 sheet: -1.13 (0.36), residues: 174 loop : -1.09 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 704 TYR 0.023 0.001 TYR C 382 PHE 0.018 0.001 PHE C 374 TRP 0.012 0.001 TRP A 336 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (14110) covalent geometry : angle 0.57484 / 0.29 (19170) hydrogen bonds : bond 0.03770 / 2.60 ( 578) hydrogen bonds : angle 4.54189 / 3.15 ( 1612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8632 (t0) cc_final: 0.8216 (t0) REVERT: A 48 MET cc_start: 0.7798 (ppp) cc_final: 0.7437 (ppp) REVERT: A 163 GLU cc_start: 0.8961 (tp30) cc_final: 0.8528 (tp30) REVERT: A 365 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: B 393 MET cc_start: 0.7833 (tpt) cc_final: 0.7616 (tpt) REVERT: B 422 ASP cc_start: 0.8624 (p0) cc_final: 0.8377 (p0) REVERT: B 499 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7793 (m) REVERT: B 503 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8287 (mpp) REVERT: B 686 ARG cc_start: 0.8710 (mmt-90) cc_final: 0.8414 (mmm160) REVERT: C 210 GLU cc_start: 0.7927 (mp0) cc_final: 0.7599 (mp0) REVERT: C 423 GLN cc_start: 0.7934 (tp40) cc_final: 0.7644 (tp-100) REVERT: C 472 GLU cc_start: 0.8532 (pt0) cc_final: 0.8310 (pp20) outliers start: 22 outliers final: 14 residues processed: 197 average time/residue: 0.1264 time to fit residues: 35.8363 Evaluate side-chains 196 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089033 restraints weight = 50120.005| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.88 r_work: 0.2877 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14110 Z= 0.192 Angle : 0.587 9.755 19170 Z= 0.294 Chirality : 0.042 0.164 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.524 73.406 2033 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.60 % Allowed : 11.82 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1653 helix: 1.29 (0.20), residues: 735 sheet: -1.15 (0.36), residues: 174 loop : -1.09 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 704 TYR 0.021 0.001 TYR C 382 PHE 0.019 0.001 PHE C 374 TRP 0.013 0.001 TRP A 336 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (14110) covalent geometry : angle 0.58689 / 0.29 (19170) hydrogen bonds : bond 0.03774 / 2.59 ( 578) hydrogen bonds : angle 4.51377 / 3.14 ( 1612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8695 (t0) cc_final: 0.8271 (t0) REVERT: A 48 MET cc_start: 0.7895 (ppp) cc_final: 0.7606 (ppp) REVERT: A 163 GLU cc_start: 0.8991 (tp30) cc_final: 0.8556 (tp30) REVERT: A 365 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: B 499 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.7911 (m) REVERT: B 503 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8315 (mpp) REVERT: B 686 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8420 (mmm160) REVERT: C 210 GLU cc_start: 0.7922 (mp0) cc_final: 0.7633 (mp0) outliers start: 24 outliers final: 16 residues processed: 196 average time/residue: 0.1299 time to fit residues: 36.9575 Evaluate side-chains 198 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 125 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 0.0270 chunk 8 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.091171 restraints weight = 39465.365| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.29 r_work: 0.2943 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14110 Z= 0.128 Angle : 0.558 9.309 19170 Z= 0.280 Chirality : 0.041 0.158 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.436 73.483 2033 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.27 % Allowed : 12.48 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1653 helix: 1.36 (0.20), residues: 735 sheet: -1.05 (0.36), residues: 174 loop : -1.07 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 704 TYR 0.021 0.001 TYR C 382 PHE 0.019 0.001 PHE C 41 TRP 0.012 0.001 TRP A 336 HIS 0.005 0.001 HIS C 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (14110) covalent geometry : angle 0.55808 / 0.28 (19170) hydrogen bonds : bond 0.03491 / 2.40 ( 578) hydrogen bonds : angle 4.39926 / 3.05 ( 1612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8698 (t0) cc_final: 0.8246 (t0) REVERT: A 48 MET cc_start: 0.7845 (ppp) cc_final: 0.7608 (ppp) REVERT: A 163 GLU cc_start: 0.8923 (tp30) cc_final: 0.8463 (tp30) REVERT: B 140 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 436 MET cc_start: 0.8818 (ttt) cc_final: 0.8556 (ttp) REVERT: B 503 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8528 (mpp) REVERT: B 686 ARG cc_start: 0.8655 (mmt-90) cc_final: 0.8396 (mmm160) REVERT: C 423 GLN cc_start: 0.7853 (tp40) cc_final: 0.7609 (tp-100) outliers start: 19 outliers final: 15 residues processed: 197 average time/residue: 0.1204 time to fit residues: 34.6176 Evaluate side-chains 194 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 0.0020 chunk 162 optimal weight: 10.0000 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 604 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 = 0.3605 r_free = 0.3605 target = 0.122754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091451 restraints weight = 43079.393| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.50 r_work: 0.2946 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14110 Z= 0.112 Angle : 0.557 9.271 19170 Z= 0.277 Chirality : 0.041 0.175 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.349 73.874 2033 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.54 % Allowed : 12.88 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1653 helix: 1.41 (0.20), residues: 735 sheet: -0.94 (0.36), residues: 173 loop : -1.06 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 704 TYR 0.023 0.001 TYR C 382 PHE 0.020 0.001 PHE B 290 TRP 0.012 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (14110) covalent geometry : angle 0.55656 / 0.28 (19170) hydrogen bonds : bond 0.03334 / 2.31 ( 578) hydrogen bonds : angle 4.34870 / 3.02 ( 1612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8712 (t0) cc_final: 0.8244 (t0) REVERT: A 48 MET cc_start: 0.7895 (ppp) cc_final: 0.7670 (ppp) REVERT: A 163 GLU cc_start: 0.8960 (tp30) cc_final: 0.8483 (tp30) REVERT: A 451 MET cc_start: 0.9210 (mtt) cc_final: 0.8744 (mtt) REVERT: B 140 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8162 (tm-30) REVERT: B 283 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8382 (tppt) REVERT: B 503 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8539 (mpp) REVERT: B 551 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: B 686 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8408 (mmm160) REVERT: C 364 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8145 (mtm-85) REVERT: C 423 GLN cc_start: 0.7843 (tp40) cc_final: 0.7580 (tp-100) REVERT: C 472 GLU cc_start: 0.8467 (pp20) cc_final: 0.8173 (pp20) outliers start: 23 outliers final: 16 residues processed: 198 average time/residue: 0.1136 time to fit residues: 32.7452 Evaluate side-chains 196 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 131 optimal weight: 0.0980 chunk 146 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092098 restraints weight = 34634.435| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.19 r_work: 0.2960 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14110 Z= 0.108 Angle : 0.550 9.097 19170 Z= 0.276 Chirality : 0.041 0.267 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.276 74.322 2033 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.27 % Allowed : 13.22 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1653 helix: 1.43 (0.20), residues: 735 sheet: -0.83 (0.36), residues: 173 loop : -1.03 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 704 TYR 0.038 0.001 TYR C 179 PHE 0.020 0.001 PHE B 290 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14110) covalent geometry : angle 0.55018 / 0.28 (19170) hydrogen bonds : bond 0.03241 / 2.26 ( 578) hydrogen bonds : angle 4.29556 / 2.98 ( 1612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8694 (t0) cc_final: 0.8190 (t0) REVERT: A 48 MET cc_start: 0.7885 (ppp) cc_final: 0.7639 (ppp) REVERT: A 163 GLU cc_start: 0.8893 (tp30) cc_final: 0.8423 (tp30) REVERT: B 140 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8181 (tm-30) REVERT: B 283 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8380 (tppt) REVERT: B 503 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8493 (mpp) REVERT: B 686 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.8373 (mmm160) REVERT: C 423 GLN cc_start: 0.7853 (tp40) cc_final: 0.7592 (tp-100) REVERT: C 472 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8162 (pp20) outliers start: 19 outliers final: 15 residues processed: 194 average time/residue: 0.1037 time to fit residues: 29.4305 Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 472 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 475 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.087410 restraints weight = 56741.883| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.01 r_work: 0.2879 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14110 Z= 0.155 Angle : 0.575 8.710 19170 Z= 0.289 Chirality : 0.042 0.270 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.327 74.015 2033 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.47 % Allowed : 13.28 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1653 helix: 1.42 (0.20), residues: 736 sheet: -0.92 (0.36), residues: 174 loop : -1.04 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 704 TYR 0.022 0.001 TYR C 382 PHE 0.020 0.001 PHE C 374 TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (14110) covalent geometry : angle 0.57468 / 0.29 (19170) hydrogen bonds : bond 0.03453 / 2.39 ( 578) hydrogen bonds : angle 4.36469 / 3.03 ( 1612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8768 (t0) cc_final: 0.8263 (t0) REVERT: A 48 MET cc_start: 0.7934 (ppp) cc_final: 0.7685 (ppp) REVERT: A 103 ASP cc_start: 0.8450 (t0) cc_final: 0.8168 (p0) REVERT: A 163 GLU cc_start: 0.8942 (tp30) cc_final: 0.8504 (tp30) REVERT: A 451 MET cc_start: 0.9205 (mtt) cc_final: 0.8738 (mtt) REVERT: B 140 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 283 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8409 (tppt) REVERT: B 499 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8181 (p) REVERT: B 503 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8658 (mpp) REVERT: B 551 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: B 686 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8417 (mmm160) REVERT: C 364 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: C 423 GLN cc_start: 0.7916 (tp40) cc_final: 0.7656 (tp-100) REVERT: C 472 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8238 (pp20) outliers start: 22 outliers final: 16 residues processed: 191 average time/residue: 0.1088 time to fit residues: 30.3204 Evaluate side-chains 194 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 472 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 161 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091932 restraints weight = 33839.394| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.11 r_work: 0.2968 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14110 Z= 0.109 Angle : 0.555 8.838 19170 Z= 0.279 Chirality : 0.041 0.253 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.262 74.500 2033 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.20 % Allowed : 13.62 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1653 helix: 1.42 (0.20), residues: 735 sheet: -0.81 (0.36), residues: 173 loop : -1.04 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 704 TYR 0.023 0.001 TYR C 382 PHE 0.020 0.001 PHE C 374 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14110) covalent geometry : angle 0.55472 / 0.28 (19170) hydrogen bonds : bond 0.03208 / 2.22 ( 578) hydrogen bonds : angle 4.29317 / 2.98 ( 1612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.16 seconds wall clock time: 51 minutes 35.06 seconds (3095.06 seconds total)